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Best accounting software for Shopify users

Susan Honea

Susan Honea – 8 years experience helping businesses with bookkeeping, tax preparation and auditing

Last updated: September 17, 2020

Trying to find the right accounting software which you can integrate with Shopify? In this article, we reveal the best accounting software for Shopify in 2020.

Best accounting software for Shopify users

As a Shopify store owner, you’re a creator, not an accountant, but that doesn’t mean that the accounting tasks aren’t required for your business. Shopify store owners need to understand and manage cash flow, send invoices and take payments, track expenses, manage inventory, and run reports, among other things.

The accounting software you choose needs to be one that works for you, not the other way around. Accounting software needs to be easy for the Shopify seller to set up and navigate, and it should have some element of automation that minimizes the hassle of day to day accounting tasks. Your Shopify store’s total transaction volume and income will probably help you narrow your choices, too. If you have multiple Shopify stores, you’ll want to make sure that your accounting solution can handle multiple entities, and several of our choices for best accounting software for Shopify do. Plus, there are a few options on this list that even have bookkeeper support if you need it.

An important feature that Shopify users should look for in accounting software is a clean integration, which allows data to flow from Shopify into the accounting software itself. In some cases, this connection is native, meaning it was created by the accounting software developer. In other cases, the connection is managed by a third party. For each product on our list, we’ve noted which method is available and whether any major issues have been reported. The Shopify app store is a good source of information for user ratings, and many of the apps offer free trials, so you can choose the one that works best for you before making a purchasing decision.

Shopify users may also need to track sales taxes (what’s been collected and what’s due to the state in which the user has nexus). While we can’t provide advice about whether you’re required to collect and remit sales taxes, Shopify can be configured to collect sales tax automatically, so what’s important here is whether the accounting software you choose facilitates tracking the remittance information easily.

Read on to learn more about the accounting software we have identified as best options for Shopify store owners.

Best accounting software for Shopify sellers: the snapshot

We found these to be the best accounting options for Shopify sellers:

  1. Xero. Best overall accounting software for Shopify users. Xero comes with strong accounting functionality and helpful mobile capability. Its scalability makes it a good option for Shopify store owners hoping to grow their online stores. Xero is known for its expansive integration options, and provides third party app choices to integrate seamlessly with Shopify.
  2. QuickBooks Online. Most comprehensive accounting software for Shopify users. QuickBooks ends up on most best accounting software lists because it is a proven accounting solution that typically exceeds the needs and expectations of small business owners, and the Shopify store owner’s experience should be no different. Like Xero, QuickBooks relies on third party apps to integrate with Shopify.
  3. FreshBooks. Best accounting software for Shopify users on the go. Shopify store owners interested primarily in invoicing and expense tracking that would also like basic accounting tools, too should look at FreshBooks. With its strong project management functionality, it’s a good option for sellers with projects to manage, and it integrates easily with Shopify through its own native app or through a third-party app.
  4. Sage 50cloud. Best accounting software for Shopify users with bookkeeping experience. For the Shopify store owner in need of multi-entity capability, Sage 50cloud is a strong, flexible accounting software contender. It’s a powerful option for growing businesses but may require at least a little bookkeeping experience, probably more so than other products on this list. Like most products here, Sage 50cloud integrates with Shopify through a third-party app.
  5. Bench.co. Best accounting software for Shopify users who want integrated bookkeeping support. Do you find the thought of having someone else keep the books for you appealing? If so, you might want to consider Bench. This accounting software comes with a team of bookkeepers to manage your books, but they only take care of core accounting functions. You will need to do your own invoicing, and Bench doesn’t provide some of the extras many competitors on this list provide, like invoicing, inventory management, project tracking, and so on. Bench does provide its own app for integration with Shopify.
  6. Wave. Most cost-effective accounting software for Shopify users. Wave is the only free option on this list, but don’t let that fool you. Wave is a robust accounting option rich in features to meet most of the needs of a Shopify store owner. Wave provides direct integration with Shopify, and its app provides real-time order syncing automatically. The app does cost, and cost is based on the number of orders.
  7. Zoho Books. Best accounting software for Shopify users in the Apple ecosystem. Zoho Books can stand alone or be used within the Zoho ecosystem. It’s a strong, scalable accounting option, and Shopify store owners might like the extra features ZohoBooks provides. Zoho Books can be integrated with Shopify through third-party apps, plus there’s an Inventory module native to Zoho that integrates with Shopify for strong inventory management.
  8. Holded. Best accounting software for Shopify users who need a full ERP solution. Holded is more than accounting software. It’s probably more accurate to think of it as an ERP solution that includes accounting functionality. The biggest selling point here might be Holded’s claim that Shopify owners can manage their stores from within the Holded software.
  9. Versa Cloud ERP. Best accounting software for Shopify users who need multi-currency support. Like Holded, Versa Cloud ERP is a full enterprise planning resource software option. Shopify store owners in need of multi-entity and multi-currency support will want to consider Versa Cloud ERP. In addition, Versa provides a native app in the Shopify store.
  10. Craftybase. Best accounting software for Shopify users with unique inventory needs. Craftybase was designed for those who manufacture and sell handmade items. With its inventory and product emphasis, strong pricing support through the calculation of COGS, it provides some unique features that will appeal to its target demographic among Shopify store owners. Craftybase can import data directly from Shopify through its “Sales Channels.”

Best accounting software for Shopify sellers

1. Xero

Website www.xero.com
Price from $12/mo
Free Trial 30 days

Best overall accounting software for Shopify users.

Best for:
With its comprehensive accounting capabilities, strong automation features, extensive integrations, and scalability, Xero is the best overall option for Shopify store owners starting small but intending to grow. Shopify business owners who need strong mobile functionality will definitely want to consider Xero.

Key features:
With its extensive third-party app integration smorgasbord, Xero can do just about anything the Shopify store will need via its 700+ possible options. Its core accounting features include double-entry accounting, along with a customizable chart of accounts.

Xero streamlines the invoice creation process by allowing the store owner to create and save invoices as templates that can be edited or updated at any time. Xero also gives users the option of automating invoices, meaning you can set Xero to automatically create and send invoices to repeat customers.

Xero allows customers to pay directly via the invoice itself once a payment service has been integrated. The user can send a customer multiple invoices at a time to reduce clutter and confusion. It is also possible to forward fees and expenses directly to the customer when you formulate bills and receipts.

Xero offers comprehensive accounts payable functionality, and payments can be scheduled ahead of time. Bills can be emailed to the files inbox for easy filing and quick access.

Bank connections are easy with Xero, with an automatic matching option. Xero can alert you to new transactions coming into the account.

Xero’s inventory management system allows you to record inventory and monitor inventory changes on a daily basis. You can also calculate the value of goods in inventory automatically using Xero’s Simple Tracking software. The Simple Tracking software also allows for users to quickly upload information from any spreadsheet software.

Xero provides fully customizable reporting options with all the reports a business would need. Customized reports can be set as defaults for rapid updating as needed.

Shopify integrates with Xero via one of many third-party apps, including highly-rated apps from developers such as A2X, Parex Technologies, Webgility, OneSaas, and BOLD. Xero seems to connect seamlessly with Shopify. The Xero App Marketplace highlights the use of A2X for integrating Xero and Shopify to post sales automatically to Xero and reconcile accounts.

Inputting sales tax calculations is easy with Xero, allowing you to automatically figure sales tax rates. You can also figure different rates, such as different state taxes or sales taxes. There is a function for setting a Standard or default rate for your sales and purchases which can be calculated automatically, too. Xero also features an automated sales tax return function, facilitated through Avalara Trustfile, a partnered and integrated software.

Xero features an option to record and manage assets and monitor their depreciation. Project, billable expense, time, and mileage tracking are also possible with Xero although it requires a third-party app. Billable expense tracking requires the Established plan (see below), as does time tracking. Time tracking is also possible through a third-party app like Harvest.

Ease of use: 
Even among those with no accounting experience, Xero is widely considered easy to learn and navigate. The customizable dashboard helps users set up the software in a personally intuitive way. Automation simplifies daily tasks. Guides and training materials provide most of the customer support available, though.

Xero has pricing packages optimized for businesses throughout their growth process, meaning that the entry-level plan suits a business early on, the next tier is aimed at growing businesses, and the top tier plan is suitable for an established business. All of them are paid for with a monthly subscription, with the Early Business plan being the cheapest and the most limited, restricting the amount of invoices, quotes, and bank transaction reconciliations the user can do per month. The Growing plan allows for unlimited invoices, quotes, and bank transaction reconciliations. The Established plan is the only plan that allows multi-currency functions, and the ability to track expenses as well as track the time and costs of projects. There is also a free 30 day trial option to take advantage of before committing.

A2X, which is used to connect Xero to Shopify, also brings a monthly cost. Tiers—ranging from Mini to Advanced—increase in price with number of orders. Only the Advanced plan allows more than one Shopify store (up to five).

Things we liked:

  • Strong cash flow reporting
  • Invoice workflow automation
  • Variety of app integrations
  • Clean, intuitive navigation
  • Mobile app

Things we didn’t like:

  • Expensive for high volume sellers
  • Poor customer support
  • Limited multi-currency support

2. QuickBooks Online

Price from $25.00/mo
Free Trial 30 Days

Most comprehensive accounting software for Shopify users.

Best for:
QuickBooks Online offers a range of packages with various sets of features, making it suitable for many kinds of businesses. It’s flexible and scalable, so it should make the cut for any short list, whether you’re a microbusiness, small business, or medium-sized entity. Built with bookkeepers in mind originally, QuickBooks Online has become a versatile and flexible accounting option, coming in at various price points.

Key features:
QuickBooks Online is a cloud-based option with strong mobile functionality through its iOS and Android apps. All basic accounting functions are available at most tiers, except for Self Employed, which is limited. The tiers including Simple Start and beyond include double-entry accounting functionality that should meet the needs of most Shopify sellers.

The Shopify store owner will find the QuickBooks Online invoicing workflow customizable in that estimates can be converted to invoices and, beginning with the Plus subscription, can be set to recur. QuickBooks Online accepts all credit cards through QuickBooks Payments and can also do bank ACH transfers. Customers can pay directly from the invoice, which provides the ability to track the payment status of invoices and send reminders or connect payments to invoices automatically. Online payment options include Stripe, Square, and PayPal, which all integrate seamlessly with QuickBooks Online.

QuickBooks Online provides strong machine learning capabilities when bank feeds are set up, including feeds for payment processors, such as Stripe, Square, and PayPal. Rules can be set for specific transactions, saving time and reducing errors. Shopify store owners can use the mobile app to snap pics of receipts, and QuickBooks Online can match them automatically. Custom expense categories are easy to set up, and the bill payment feature is flexible, allowing the store owner to schedule payments in advance, set them to recurring, and make online payments directly from QuickBooks Online.

Shopify retailers will find that QuickBooks Online provides inventory management at the Plus and Advanced levels, along with Cost of Goods Sold tracking. The low inventory level notification is automatic, and inventory reports allow the store owners to see easily what is selling and what’s not. QuickBooks Online also offers purchase order capability. Purchase orders can be imported directly from Shopify or from Excel.

The Shopify retailer can easily create most of the reports (customized) needed for keeping the books, including profit and loss, expenses, and balance sheet reporting, starting at the Simple Start level. At the Essentials level, store owners will find sales, receivable, and payables reporting functionality. Inventory reports, comprehensive sales, and profitability reports are available with the Plus plan. If the store owner wants comprehensive reporting functionality, that will require the Advanced plan. QuickBooks Online mobile apps make many reports available, too.

QuickBooks Online connects to a variety of e-commerce applications including Shopify when tracking sales. Third-party apps available in the Shopify App Store to connect QuickBooks Online include those from BOLD, Webgility, OneSaas, Parex Technology, Flowify, and A2X.

Automatic sales tax tracking and calculation is available at all price points. QuickBooks Online also helps with easy organization of tax information. Sales tax is automatically calculated on any invoice.

Shopify store owners in need of mileage tracking will find that feature in QuickBooks Online, along with time tracking at the Essential tier, including integrated time trackers. The Essentials plan allows multiple concurrent users, but limits the number of concurrent users to three.

Multi-user functionality is available at the Plus plan level and up. QuickBooks Online Plus also provides bill management, project profitability tracking, budgeting, and inventory management. This level allows five concurrent users. Shopify retailers who need bill pay, batch processing, and role-based permissions will need to subscribe to the Advanced plan (the highest level). This plan allows 25 concurrent users, as well. Shopify retailers with more than one store to manage should be aware that no version of QuickBooks Online offers multi-entity support.

Ease of use: 
Potential users who want to find out just how easy QuickBooks Online is to navigate can go to the website and take a test drive online using a sample company. QuickBooks Online is a user-friendly option that is also flexible with lots of add-ons available. Because QuickBooks is so popular, it’s easy to find help with it. Not only is there a QuickBooks Online User Community, but there are a multitude of other options available to help the Shopify retailer hit the ground running with this accounting software: webinars, video tutorials, training classes, and even paid training opportunities.

There are four tiers of the software available. The lowest is the “Simple Start” tier which allows only basic functions. The other three are the Essentials tier, the Plus tier, and the Advanced tier. There is also a separate Freelancer package (Self Employed) that allows for only the bare minimum of functionality, but it is cheap, which may be tempting to Shopify users just getting started.

Things we liked:

  • Simple setup process
  • Strong support in user community
  • Excellent reporting capability
  • Good mobile apps
  • Robust machine learning features

Things we didn’t like:

  • Inventory management is costly
  • No multi-entity support
  • May be too much functionality

3. FreshBooks

Price from $15/mo
Free Trial 30 days

Best accounting software for Shopify users on the go. 

Best for:
FreshBooks is a popular option among many types of small businesses. It’s a go-to product for many self-employed business owners. Shopify store owners who need primarily invoicing and expense tracking or need to manage multiple projects will want to take a look at FreshBooks.

Key features:
FreshBooks has all the basic double-entry accounting features a Shopify retailer would need, and they are laid out plainly so that it is easy for even people with little to no understanding of accounting to use. Automations add to FreshBooks’s appeal. Automation is available for bank reconciliations and in the form of a checks and balances system that compares debit and credit amounts, helping users save time and make fewer errors.

FreshBooks provides effective bank integration, and the bank reconciliation process is easy with FreshBooks. Reconciliation takes place as transactions are downloaded. Some business owners, especially those with bookkeeping experience, may miss a more detailed, formal reconciliation process with a month-end close, but all in all, FreshBooks’ reconciliation process is probably enough for most Shopify retailers.

FreshBooks specializes in automatic invoice creation and allows users to set billable hours to attach to invoices. Client info can also be set to automatically be added to invoices. Users can also set recurring invoices for regular customers. In addition, invoices are customizable. The sales process flows easily from proposals and estimates to invoices. FreshBooks includes a helpful retainer function for accepting advanced payments and applying them automatically to the invoicing workflow.

Invoicing and payment collection can be done through FreshBooks’s software or through an integration with Stripe. FreshBooks also provides multi-currency support, which is helpful to Shopify retailers selling internationally. Advanced plans can add late fees and automatic reminders.

FreshBooks partners with Yodlee for bank, credit card, and PayPal feeds in the U.S., but Canadian, Australian, and most European users will use Plaid or Salt Edge. Once an account is connected, FreshBooks can remember and automatically categorize expenses and transactions coming in.

Tracking expenses and billable expenses is simple with FreshBooks’s bank integration. FreshBooks can add your expenses to your bank registers automatically each day, and it learns to categorize expenses automatically, as well, which makes tax prep easier at the year’s end. The retailer can attach pictures of receipts, too.

Shopify retailers who need to manage inventory will have to integrate FreshBooks with either 2Ship or BarCloud. However, that may be enough functionality to manage inventory in Shopify.

FreshBooks can create profit and loss, trial balance, accounts aging, sales tax, and invoice reports, among others, by client, team member, or date. In addition, FreshBooks provides a real-time breakdown of your spending and other business activity, making it easy to keep track of data.

FreshBooks has built its own app for integration with Shopify. Once the two are synced, all of the products, orders, and payments received in Shopify are imported into FreshBooks. If, for some reason, a store owner isn’t happy with the FreshBooks app, other third-party apps are available in the Shopify App Store from OneSaas and CarryTheOne.

The Shopify store owner using FreshBooks can set up the sales tax for products under the company settings and can set up as many different tax rates as are necessary for the specific company. FreshBooks automatically keeps track of sales tax information in a “Sales Tax Summary.” FreshBooks can also auto-generate reports of sales tax information, making filing easy.

FreshBooks enables project tracking and makes it easy to assign projects to clients and teams. Other tracking features include time and mileage, which can both be tracked by client or project. FreshBooks also comes with excellent contact management tools.

Ease of use: 
FreshBooks specializes in ease of use and automation. It was initially designed for invoicing with a target demographic of business owners, so it doesn’t require in-depth accounting knowledge to use. Only recently has double-entry accounting been added to the software, but it is still intuitive and easy to use. FreshBooks is also known for its friendly and helpful customer service committed to helping users succeed with the software.

There are three tiers available. The cheapest of them is the Lite package which gives unlimited customizable invoices, expense entries, estimates and time tracking. In addition, with the Lite package, you are limited to only 5 billable clients. The Plus and Premium tiers allow for more billable clients and the ability to create automatic invoices for recurring clients. You can also add more team members to your account with any tier, but it costs an additional $10 per person added.

There is also the “Select” package which allows for custom pricing based on the needs of your business. When selecting this option, you are given access to a personal Account Manager and customized training in the use of FreshBooks. There is also cross-integration between this platform and QuickBooks and Xero.

No matter what package you choose, each one includes automated bank imports, although, as noted, automated invoice creation is limited to the Plus package and higher. If you elect to go with the Select package, you can also get in touch with an Account Manager, who can help you select what tools and apps to use for your business. All plans come with a 30-day money-back guarantee.

Things we liked:

  • Excellent mobile functionality
  • App integrations
  • Super-simple to use
  • Great customer service
  • Multi-currency options

Things we didn’t like:

  • Multi-user pricing gets expensive quickly
  • Limited reporting capabilities
  • Not necessarily designed for retailers

4. Sage 50cloud

Score 6
Price from $50.58/mo

Apps Available

Special Deal

Save 40% on the annual subscription

Best accounting software for Shopify users with bookkeeping experience.

Best for:
Entities wanting a robust and flexible, proven option with a four decade track record will need to take a look at Sage 50cloud. It’s ideal for a business with an accountant or accountants onsite. The three Sage 50cloud subscriptions available are each specialized for either freelancers/solopreneurs, a business with a team of 1-5, or a business with up to 40 users.

Key features:
Sage 50cloud offers full double-entry accounting. Income and expenses functionality is robust. In fact, Sage 50cloud has it all, and it integrates with Shopify via a third party app from eBridge Connections. Though the Shopify integration is fairly pricey and may be cost prohibitive for retailers dealing in lower volumes, users who need strong accounting functionality will appreciate Sage 50cloud’s comprehensiveness.

Invoices templates are easy to customize, duplicate, and set to recurring. Sage 50cloud has a feature where quotes and proposals can automatically convert into invoices when you follow through with a customer. Sage 50cloud also integrates smoothly with Microsoft Office 365, and invoices can be sent out via Outlook. Sage 50cloud allows you to easily process and keep track of payments as you receive them. In addition, Sage 50cloud payments allow immediate payment from invoices, but this feature does cost extra. If you’re using Shopify to process your payments, this shouldn’t be an issue.

For expense tracking, users will need to manually categorize expenses. Once categorization is done, Sage 50cloud—which can be connected to banking accounts for automatic importation of transactions—can reconcile transactions quickly and easily.

Sage 50cloud comes with very good inventory tracking capability and excellent CRM and Customer Management functionality. A lot of specific data can be tracked for each inventory item. Tracking allows multiple price levels per item, too.

Sage 50cloud can generate reports on various figures, from sales tax to expenses to profits with a simple click. Reports can be customized. A nifty feature of Sage 50cloud reports is that they are interactive, so users can click into entries (drill down) for additional detail. The dashboard provides real-time information, such as case available, expenses, receivables, and inventory.

All Sage products ensure full compliance with tax laws. Sales tax can be tracked in each customer’s account and set uniquely by customer. Sales tax reporting is also available. Similarly, payroll and direct deposits are available as add-ons and do cost extra. Other add-ons provide access for multiple users, tax return e-filing, and training through Sage University online.

One note of caution is that Sage50 lacks strong mobile apps and really isn’t a great choice for Shopify users on the go. Similarly, though it is technically cloud-based, users will quickly find out that a desktop installation is required to use all of Sage 50cloud’s features.

Ease of use: 
Sage 50cloud provides an easy set up experience, but probably presents somewhat of a learning curve for those with no bookkeeping or accounting experience. Online tutorials and graphic workflows at the Sage website are helpful, but users shouldn’t expect a lot of support here. Sage 50cloud isn’t ideal for mobile access as its apps are limited and the browser is the best way in.

Customers have the option to choose between yearly or monthly subscriptions. There are three packages available, each one optimized for a different setup. The cheapest tier is geared towards solo users such as entrepreneurs. The middle tier is for business with 1-5 users. The final tier is made for sizable business with a maximum of 40 users. This last iteration features specializations for construction, distribution or manufacturing businesses. Updates and upgrades can be costly, and additional features (including budgeting, multi-entity support, and specific user permissions) add to the cost.

Things we liked:

  • Robust accounting functionality
  • Multi-entity options
  • Excellent compliance features
  • Comprehensive reporting module
  • Integrates with Office 365

Things we didn’t like:

  • Outdated interface
  • No mobile apps
  • Expensive

5. Bench.co

Website Bench.co
Price from $139/mo

Best accounting software for Shopify users who want integrated bookkeeping support. 

Best for:
Those who don’t have any accounting knowledge, are not comfortable with bookkeeping, or not willing to invest the time needed for keeping the books should consider Bench. It’s more of a bookkeeping service than an accounting software option, but there is software involved!

Key features:
Unlike other accounting software offerings, Bench provides a service for which the customer contacts Bench directly and meets one-on-one with a certified, professional bookkeeper who then provides accounting services for the business. Typically, Bench bookkeepers work with cash basis accounting, but accrual accounting is also available, which is important for any Shopify store owner who carries inventory. All core accounting work is handled by the bookkeeper, who works for Bench. Bench also provides a number of free downloadable guides and templates for things like taxes and invoices to help inexperienced entrepreneurs.

Bench provides a native app in the Shopify app store, making the connection between the two fully integrated. Bench’s software will automatically download all transactions so that the bookkeeper can categorize and organize them. The Shopify store owner can drag invoices and receipts into a documents section and leave them for the bookkeeper to review. The Bench bookkeeper also takes care of reconciling transactions, along with reporting, at the end of the month. The Bench software dashboard provides real-time tracking for cash flow, so that Shopify users always know where they stand.

The Shopify store owner is still responsible for preparing and sending invoices to clients. Therefore, store owners may need to use another option for invoicing if they need help tracking payments, including outstanding payments, but users who take payments through Shopify itself won’t have to worry about this issue. The Bench app integrates with Stripe, Square, banks, and credit cards, which streamlines the download process and ensures that the Bench bookkeeper has everything necessary to complete month-end reporting.

Bench software does not include inventory management capability, so Shopify store owners with inventory to track may want to look elsewhere for bookkeeping help. Smaller store owners may find that Shopify’s built-in inventory management capabilities are enough for their needs, and the Bench bookkeepers should be able to enter period-ending journal entries to adjust for inventory totals, which is important for tax preparation purposes.

A feature called the “Pulse” allows users to see business data in real time. Bench provides Shopify store owners with an end-of-year summary, too, which helps with tax preparation and planning for the future. In addition to Bench’s bookkeeping services, they also offer support aimed exclusively towards tax filing for small businesses. BenchTax is the service by which a customer can get assistance with filing taxes.

Bench doesn’t provide project tracking, but most Shopify users likely won’t find that limitation problematic. Store owners who need to track billable expenses, time, and mileage will need to find apps for these functions. Larger store owners who need to run payroll are in luck, though, as Bench integrates with Gusto for payroll even though it doesn’t offer built-in payroll functionality.

Ease of use: 
Bench is very easy for customers to use. Rather than requiring the customer to handle their own bookkeeping, Bench provides expert bookkeepers to take care of the customer’s accounting for them.

Bench offers annual and monthly payment plans that actually aren’t as expensive as one might expect. There are five different payment tier options, each one is optimized for a different level of business. The cheapest is for small starter businesses while the largest is for corporations. Bench also offers the option to recommend a package based on your business’s monthly expenses.

Things we liked:

  • No accounting experience required
  • Store owner can focus on operations
  • Strong year-end reporting
  • Native integration with Shopify
  • Real-time cash flow data

Things we didn’t like:

  • Bookkeepers can get backed up
  • Expensive compared to other options
  • No android app

6. Wave

Price from FREE/mo

Most cost-effective accounting software for Shopify users.

Best for:
Those on a budget who have a good understanding of bookkeeping will enjoy Wave’s surprising robustness at such an affordable price—it’s free (for real). Most small Shopify store owners will find that the free version is plenty of accounting support.

Key features:
With double-entry accounting, Wave allows its users to record income and expenses displayed through the chart of accounts, prepare and send invoices, complete journal transactions, and use professional-approved double-entry software. Shopify store owners will appreciate the ability to have unlimited clients, invoices, and expenses as well as many other helpful features, including multi-entity support.

Wave’s invoicing workflow makes entering, sending, and receiving payment against invoices a breeze, and Wave features unlimited invoice customization. In addition, users can also set up recurring invoices for repeat customers. Users can also set up invoice notifications to serve as reminders.

Wave’s strong multi-currency support is a big draw for Shopify store owners with international reach. Wave also features full support for payment processors like PayPal and syncs all invoicing and payment information automatically—even automatic payment reconciliation for transactions. Wave does charge for payments, but once Payments by Wave is enabled, customers can access and pay their invoices online through a portal, using credit card or bank payments.

Along with routine expense tracking, Wave includes billable expense tracking, along with some time tracking. While these may be less important features for many Shopify store owners, those who plan to grow and perhaps hire employees along the way will likely find these features useful.

Tracking inventory is not exactly straightforward via Wave and appears to be limited to tracking the value. This requires adding an asset account for inventory and an expense account for Cost of Goods and then recording the relevant transactions accurately. As with other options on our list, this limitation may not prove insurmountable since Shopify has its own built-in inventory management platform.

Wave allows both accrual and cash basis reporting. Reports include profit and loss, trial balance, cash flow, and sales taxes. Compared to other products at its level, Wave’s reporting may seem limited, but it may be enough for most sellers, given the incentive of free software.

Wave allows for direct integration of Shopify transactions via an app called Sync to Wave (by Wave Sync) with automated real time order syncing. The app does incur a monthly fee, and plans are based on the number of orders, but there is a 7-day free trial, which should be enough time to determine if the app and Wave will work for your Shopify business.

Wave allows users to generate automatic logs of their sales tax records, which can then be exported to other software. When doing this, users can also customize sales tax rates to record multiple rates all on the same account.

Other helpful features include a business bank account available with Wave Money, which provides seamless integration between the software and the bank account; basic contact management; and payroll, which is available for those who need it but requires a monthly fee. Sellers in need of project management will probably want to look elsewhere. Shopify store owners who want to limit how much time they’re spending on accounting tasks should look at Wave’s accounting, bookkeeping, and tax support, which is available for a fee.

Ease of use:
Wave features an easy to use interface, combined with tutorials to help users acclimate to its software. However, users would probably do well to have a decent understanding of bookkeeping when using Wave.

Wave is free to download and use. Registration for an account is the only requirement, and that’s also free to do. The Sync to Wave app that integrates Wave and Shopify does require a monthly fee, but compared to other app integration options, it’s not terribly expensive.

Things we liked:

  • It’s hard to beat free
  • Unlimited transactions, clients, and receipt scans
  • Easy to setup and use
  • Sales tax/VAT recordkeeping
  • Multi-currency support

Things we didn’t like:

  • Limited mobile apps
  • Better for smaller businesses
  • Weak customer support

7. Zoho Books

Website www.zoho.com
Price from $12/mo

Best accounting software for Shopify users in the Apple ecosystem.

Best for:
Shopify users who are Apple ecosystem users will love the iOS apps available for Zoho Books and other Zoho products. In addition, Shopify sellers who want to pick and choose—or at least have access to—options beyond the core accounting features will want to look at Zoho Books. If you’re already using modules from the Zoho ecosystem, Zoho Books will integrate seamlessly with your existing Zoho modules.

Key features:
Zoho Books meets all the requirements for double-entry accounting. The dashboard provides real-time data to keep you up to date on your cash flow, expenses, sales, projects, and so on.  Zoho Books’ banking module syncs bank feeds, and reconciling the account requires a few clicks. Zoho Books learns to categorize your transactions, too, making tracking quick and easy.

Zoho Books includes many options and templates for customizing estimates and invoices. Creating invoices is easy, and invoices can be scheduled ahead of time and set to recur, as necessary. Automated reminders help keep everyone on track. The retainer feature makes invoicing retainer payments simple, so Shopify store owners who take advance payments for work (such as artists, for example) don’t have to manage those transactions manually.

Zoho Books provides expense tracking, including billable expense tracking. In addition, time can be tracked by project, which is a great feature for Shopify sellers who sell items based on time spent creating them. Zoho Books also provides a mileage tracking app for Android, iPhone, and even the Apple Watch.

An Inventory module integrates with invoicing to provide a seamless workflow to complement Shopify’s own inventory feature. The Zoho Inventory module integrates with Shopify to sync products, orders, and stock easily, with the option to add multiple stores. Zoho Inventory also allows the seller to map warehouses to Shopify locations. Zoho provides fixed asset management, too, which Shopify doesn’t provide.

There are more than 50 built-in reports available in Zoho Books. Reports can be scheduled ahead of time and automated. Customization options are wide open. No matter how you want to slice your information, Zoho Books allows you to create a report for it.

Third party apps are available at the Shopify app store to integrate the two products. However, users have reported challenges integrating Stripe and PayPal with Zoho Inventory and Shopify as a unified platform.

Zoho provides a Sales Tax module for U.S. sellers. The module allows the seller to create taxes and add operations such as assigning a group, authority, rate, and exemption. Individual customers can be noted as non-taxable. Zoho Sales Tax tracks it and tells you how much you owe—you can then can record tax payments as they’re made.

Shopify sellers who need contact management for customers and vendors will not be disappointed with that feature in Zoho Books. A Client Portal provides client access to business transactions for not only viewing but accepting estimates and paying invoices. Client email templates provide easy access to that alternative when necessary.

Project management is facilitated through project dashboards and includes a timesheet workflow, billable expense tracking, project time tracking, and budgeting features. Projects can be billed by fixed cost, hour, task hour, or staff hours. In addition, the Zoho Payroll module can be added as needed and set to automatically record payroll in specified accounts.

Shopify sellers on the go will love the Zoho Books mobile app. While Zoho is best known for its iOS apps (even for the Apple Watch), the Zoho Books Android app is also excellent.

Ease of use:
Zoho Books is widely considered easy to learn and use. Again, any Shopify seller already using software from the Zoho ecosystem will certainly find Zoho Books simple to implement and learn. Those who aren’t in the Zoho ecosystem may experience a little bit of a learning curve, but its flexibility and comprehensiveness will likely outweigh any challenges in this regard.

It’s not the cheapest or most expensive accounting product on the market. How much you spend will depend upon how far you go into the ecosystem. Do you want a stand-alone accounting software or do you want to add-on the other helpful modules Zoho provides? You have options with Zoho Books, which impact how much you spend. It’s possible to find the right plan at the right price with the right features.

Things we liked:

  • Comprehensive, flexible platform
  • Responsive customer service
  • Strong mobile apps
  • Full ecosystem available
  • Relatively cost-effective

Things we didn’t like:

  • Not designed for sellers with multiple shops
  • Bank feed sometimes is glitchy
  • May be too much functionality for smaller sellers

8. Holded

Website www.holded.com
Price from FREE/mo
Free Trial 14 days

Best accounting software for Shopify users who need a full ERP solution.

Best for:
Holded is a good option for Shopify store owners who need a high level business management software option. Holded combines accounting, invoicing, CRM, inventory, projects, and HR management. This integrated platform provides visibility to all business management data, allowing Shopify sellers to see—at a glance—how their business is performing. It’s also available in Spanish.

Key features:
Holded is an ERP with accounting capability. The general ledger and chart of accounts provide a quick overview of all transactions with easy access to drill down further for a more detailed view. Holded can sync with bank feeds and provides bank reconciliation functionality. Transactions can be linked to statements in the appropriate account through “magic reconciliation.”

Holded provides tons of templates for invoicing that are customizable, can be set to recur, and prescheduled. Payments come through PayPal, credit or debit card, or a bank transfer. The Shopify store owner can set up automatic payment reminders, too. Customers can log in to a portal to check their orders and payment processing.

A disadvantage of Holded is that it doesn’t have a strong accounts payable function. Shopify users will be able to import expense transactions as part of the bank feed process, and they can be categorized to flow to the chart of accounts, but users looking for true accounts payable features will likely want to look elsewhere.

Holded’s Inventory app offers a lot of flexibility to store owners looking to customize product information. The software provides real-time information about the value of merchandise available and location. Users can search by product, date, purchase type, and more. Extensive sales tracking starts with the order and follows through to shipping, and invoices can be generated automatically. Multiple stores, e-commerce tools, and warehouses can be connected. Holded also offers stock inventory alarms, letting Shopify sellers know when inventory levels are low and helping them plan for restocking.

Holded provides a real-time view of profits and losses, along with a balance sheet. The general ledger can also be used as a report if Shopify sellers want a more comprehensive view of the business. However, reporting capability is limited to these options. In addition, there is no sales tax tracking feature in Holded, so those transactions would need to be managed independently of the software.

Holded’s website notes that users can “manage all…orders and sales from Shopify without ever leaving Holded.” Holded syncs with Shopify sales, allows the store owner to manage orders from Shopify within Holded and convert them to invoices, and supports multiple Shopify accounts, all seamlessly.

Holded provides CRM software for easy review of, insight into, and contact with customers. The Project Management feature uses Kanban Boards to help users quickly identify the status of a project, progress, and issues. Project Management includes budgeting and sales, customizable templates for organization. Gantt Charts show time on each task. Holded can import information from other project management tools and even from Excel to help users get started. The Project Management app connects easily with Holded’s accounting software, too.

Holded provides HR management software that includes payroll, along with the ability to manage vacation requests and absences. Calendars keep HR up-to-date on employee activity and leave time. In addition, profiles can be set up for employees, and paperwork related to employees can be kept in the cloud. Holded HR Management also includes time tracking functionality.

One potential challenge with Holded is that it is designed and priced for UK and European users; however, with a few workarounds, it can still be a viable solution for those in the United States.

Ease of use:
With its user-friendly interface and simple setup process (you can even import your sales and invoice transactions from an existing General Journal), Holded has a fairly short learning curve. The resources available in Holded Academy also provide users with tons of information to help them get up and running.

Holded offers a 14 day free trial, which should be enough time to determine whether it’s the right product for you. Holded provides a free plan that allows a user to create and send quotes and invoices, manage purchases and expenses, and manage suppliers and clients. All pricing is in British pounds or Euros, but the cost is relatively inexpensive at the Starter and Standard levels. The Pro tier costs twice as much as Standard, but includes “magic reconciliation,” unlimited bank account syncs, a corporate portal, recurring invoicing, advanced reporting capability, and bank remittances. Holded Team (HR), Inventory, and additional users can be added on to any plan for an extra fee.

Things we liked:

  • ERP integration
  • Easy import and setup process
  • Good customer support
  • Affordable for sellers of all sizes
  • Direct integration with Shopify

Things we didn’t like:

  • Limited expense management functionality
  • No sales tax tracking
  • Designed for UK and European users

9. Versa Cloud ERP

Price from $1,800/year
Free Trial 14 Days

Best accounting software for Shopify users who need multi-currency support.

Best for:
Versa Cloud ERP is an all-in-one software designed for Shopify sellers in need of integrated multi-entity and multi-currency accounting functionality. Versa Cloud ERP is a strong contender to meet larger Shopify sellers’—and those who sell lots of products internationally—accounting software needs with its VersAccounts module.

Key features:
Versa Cloud ERP is a full-fledged ERP system that includes eight modules in its standard platform. VersAccounts’ key accounting features include a general ledger, accounts receivable and payable, cash flow management, and fixed asset management. It is designed specifically for companies that carry inventory, making it a good choice for many Shopify users, especially those that have outgrown the capabilities of other accounting-only products on this list but aren’t yet ready for a bigger ERP, such as SAP.

Transactions flow from Shopify to VersAccounts, and VersAccounts can be set to automatically create invoices for fulfilled orders, so if most of your income transactions occur in Shopify, you may not need strong manual invoicing capabilities. However, VersAccounts handles even complex invoices and batch invoicing (emailed or printed) easily. Even though Shopify payments can manage most of your order payment processing, VersAccounts facilitates payment processing in a variety of ways, including PayPal and ACH.

VersAccounts also includes accounts payable functionality. Bills can be entered as they are received, and vendor payments can be made with manual checks or ACH processing and then reconciled during month-end processing.

Versa Small Business Cloud ERP provides management of inventory for multiple locations and across multiple systems. Add-on capabilities include integration with a scanner or mobile device for tracking and managing inventory.

Standard reporting capabilities include balance sheets, income statements, aging, and others. All reports can be customized and filtered, and reports can be downloaded to Excel and other spreadsheet formats for further customization, as required.

Versa Cloud ERP integrates directly with Shopify via a native app in Shopify app store. Because the app is native, meaning that it was developed by Versa Cloud ERP, the possibility of transaction import errors is significantly minimized.

VersAccounts also tracks sales tax information from Shopify. There are some additional features in VersAccounts that larger Shopify retailers will appreciate, including matching sales tax rates between Shopify and VersAccounts and automatically creating and tracking sales tax when it’s not already on the Shopify order. Tax liabilities are tracked in the chart of accounts for payment on a monthly, quarterly, or annual basis, depending on your locality’s requirements.

Strong multi-entity and multi-currency capabilities exist in Versa Cloud ERP. VersAccounts even goes so far as to color-code the subsidiary companies on the chart of accounts, so users can easily see what information flows down to each subsidiary and up to the top-level or holding company.

Users can create dimensions and variables within each dimension, both of which are unlimited; this functionality strengthens reporting slice capabilities. Transactions can be tagged with dimensions and variables from within the transaction entry window, allowing transactions to be split—or allocated—across multiple dimensions.

Users can also create and track production orders and use the built-in CRM software that’s included to manage contacts, services, and pipelines. The projects features allow users to track, view, and report on billable and non-billable time and expenses. Purchasing and order management is built-in, as is document management, which is a nice feature for Shopify sellers who need secure document storage capabilities.

Ease of use:
Versa Cloud ERP—and VersAccounts, in particular—is user friendly, easy, and straightforward to use. The VersAccounts team provides excellent customer support, walking you through the setup and implementation process. If you’re a bigger Shopify retailer, and you require software customization, that’s available, too, and the VersAccounts team will be with you every step of the way.

Versa Cloud ERP is available for a yearly subscription fee. The interesting thing here is that pricing is based on number of users or revenue. It’s not the cheapest option in this space, but it does provide a lot of functionality, on par with much more expensive solutions. There’s a free trial period available, too.

Things we liked:

  • Native Shopify integration
  • Complete ERP platform
  • Excellent customer support
  • Multi-currency capabilities
  • Strong multi-entity features

Things we didn’t like:

  • Standard reports are basic
  • Per-user access can be expensive
  • Limited ability to process product returns

10. Craftybase

Price from $1,800/year
Free Trial 14 Days

Best accounting software for Shopify users with unique inventory needs.

Best for:
People who manufacture and sell handmade items are the target demographic for Craftybase. This inventory and bookkeeping software helps sellers price products and track inventory, and it integrates with Shopify and other online retail sites, along with Square and PayPal.

Key features:
Craftybase relies on accrual method accounting, which is necessary for most inventory-based businesses anyway. The software is focused on inventory and products. Everything connects to the stock: expenses are assigned to products, along with materials used. Craftybase makes profit explicitly clear. In addition, inventory and the manufacturing process are easy to trace.

Craftybase helps Shopify sellers with pricing for products by suggesting prices based on cost of materials and labor. It can be easy to overlook materials or other factors that affect price, and Craftybase helps with that and also with evaluating the impact using different materials might have, which can be useful when making decisions based on profitability. Craftybase emphasizes that its use of methods for calculating Cost of Goods Sold (COGS) are IRS approved and GAAP compliant. And, changes in stock, including loss or damage, are easy to track in Craftybase, and orders and products from Shopify or other sales channels are automatically imported.

Craftybase allows sellers to create and customize invoices. Sellers can add logos, add business details, set payment terms, and add custom notes to invoices. Invoices are generated in the Orders list page and then downloaded to the user’s computer as a PDF. Sellers can take payments through Shopify POS, PayPal Here, or Square POS. Craftybase integrates seamlessly with all of the methods.

Craftybase provides robust expense tracking capability—including both direct and indirect expenses. Users can either create custom and tax categories or use those established by the software. Expenses are used to calculate the COGS. The software can also draw upon expenses for real time profit margin tracking. Craftybase automatically calculates actual costs. Craftybase also allows expenses to be linked to specific individual orders or to inventory itself.

Craftybase relies on a perpetual inventory system in managing inventory, employing a Weighted Average Cost method. The software automatically calculates Cost of Goods Sold, even compiling a Schedule C Report. The Materials inventory feature allows the seller to search and sort materials and products easily. And, Craftybase also helps with tracking consignment stock and stocktaking.

The software provides the capability of setting up “recipes” by clicking options for combinations of materials commonly used, which helps the seller to determine profitable pricing for goods. Craftybase refers to the process as creating “recipes” to find out how much the cost of a product is exactly. Pricing can be assigned by retail, wholesale, consignment, and online sales.

Craftybase includes the typical bookkeeping reports a seller might need, including profit and loss, sales and expenditures, along with a Schedule C guidance report. Many reports are tailored for “small batch handmade business,” featuring Cost of Goods Sold and inventory-based reports. Craftybase makes it easy to track material costs and expenses.

Craftybase refers to online marketplaces from which it can import data, including Shopify, as Sales Channels. Craftybase can be set to update (import) automatically or users can enter the data manually, as needed (for example, to backdate historical information after implementing Craftybase). Sales Channels are easily accessed via the top navigation bar.

Craftybase does not offer an API and notes on their help page that they haven’t seen much interest in one to date. Instead, Craftybase uses Shopify API to import data from the Shopify servers. Craftybase’s access to Shopify is “read only.” One really helpful import feature is that Craftybase can import Shopify Variants, including elements such as size and color. These are imported into Craftybase as product-level variations and/or variation attributes.

Users can apply tax rates as a basis for Craftybase to calculate sales taxes. Users can set a default rate or change tax rates by order as necessary.

Craftybase does not import from bank feeds. There is a workaround of sorts that allows a user to add expenses to a template spreadsheet, export it to CSV, and then upload it to Craftybase. This approach would only be worthwhile if there are a lot of expenses to upload, and it’s only possible with the Pro or Studio account.

If you need more comprehensive accounting functionality, Craftybase allows users to export data as CSV and then import it into any accounting software that accommodates it.

Ease of use:
Craftybase is web-based and accessed via the cloud. It is available everywhere. Craftybase software provides an overview of a manufacturer/seller’s inventory, revenue, expenses, and profit. Expenses, orders, and cashflow are always visible on the My Overview (homepage) of the dashboard. Craftybase probably requires that a user learn a little about inventory bookkeeping, but this is easy enough to accomplish in just a few moments. Craftybase’s help center/knowledge base is easy to navigate and includes a wealth of information presented in easy-to-understand language. Shopify has its own page, too.

Craftybase isn’t terribly expensive, but the Starter plan is very basic, allows only one user, and requires manual entry. Reporting at this level is basic. To import expenses and run advanced reports requires the Pro plan. Like the Starter plan, the Pro plan is limited to one user, but it does also add expense importing, stocktaking, and component assemblies. The Studio plan is designed for teams and comes with two users accounts, plus three integrated sales channels, consignment tracking, multiple price points, material lot tracking, and BIN tracking.

Things we liked:

  • Designed for small manufacturers/sellers
  • Hefty inventory capability
  • Affordable at all subscription levels
  • Excellent knowledge base and support resources
  • Good tax tracking and reporting

Things we didn’t like:

  • Not full accounting software
  • No bank feeds
  • Not customizable


Why do I need accounting software with Shopify?

Granted, Shopify does a lot for the store owner. The software helps you design and set up an online store, add products to your store and organize them, choose a payment gateway, set up taxes, and identify the best shipping rates. From hosting to securing your website, Shopify does a lot for you! However, the software won’t keep your books. That’s on you. As a store owner, you will be responsible for your own bookkeeping and the financial management of your business.

Do I really need accounting software if I just have a small Shopify store?

All businesses, even the smallest ones, can benefit from accounting software. Sure, you can use spreadsheets or even paper and pencil, but those old methods take up valuable time and are more prone to accounting errors than software. Accounting software helps you save time that can be better spent on your business and/or creating new products to advance your business. Accounting software helps you keep accurate, error-free books and make certain your remain compliant with tax laws. Do you plan to grow your business? If so, you will thank yourself later for getting started with accounting software sooner!

As a store owner, I have a lot of business expenses already, and I’m not convinced I want to take on another for accounting software.

You’re in luck! Accounting software comes in a range of prices, and we have even included a free option in our reviews. Of the paid options, you will find some that are relatively cheap, and many that are scalable, meaning you can pick the package with the features you actually need. Most offer add-on features, too, that you can purchase as needed. You have options!

Do Shopify store owners need specific accounting software features?

All business owners probably need the core accounting features of accounts receivable, accounts payable (and invoicing!), reports, and bank syncing and reconciliations. You may also need project management, inventory management, sales tax features, and tracking of billable expenses, time, etc. You will need a way to process payments, too. As a Shopify seller, you will want to make sure your software integrates effectively with your store so that your transactions transfer to the software seamlessly. All of the products we have reviewed here integrate with Shopfiy, either by native app or third party. If you are considering another product not listed here, you will want to do your homework to see how it integrates (or doesn’t!) with Shopify.

Which software is the best for the Shopify store owner?

Each Shopify store owner will need to determine the essential features and base a decision on that. Again, do you need project management features? Do you have inventory to manage? Are you selling in multiple currencies? There are many factors that can impact your decision, so it’s important to start with a list of needs and go from there. We hope our reviews can provide you with a good starting point!


As a Shopify store owner, you have a lot of hats to wear. You have to keep your store stocked and running. But one thing you don’t have to do is spend hours each day recording every transaction in a spreadsheet or by paper and pencil. Instead, you can save time by implementing accounting software that can automate many tasks for you, help you stay on top of the books, and make sure your books are accurate. Running your own business is supposed to be a dream come true, and knowing your books are squared away means there is one less thing to worry about.

See also: