Great accounting software keeps Shopify businesses running smoothly, from daily operations to long-term financial health. But which to choose?

With many options out there, the real challenge isn’t finding great accounting software. It’s getting one tailored to Shopify and integrated with top-tier ecommerce accounting apps like MyWorks.

Let’s explore the best accounting software for Shopify, comparing their pros, cons, and ideal use cases.

Top Shopify accounting software compared

1. QuickBooks

While many accounting solutions have ecommerce features, only QuickBooks has dedicated plans for online merchants. You can access all the essential tools like inventory management and sales tax automation without having to pay for unnecessary extras.

Ecommerce features aside, QuickBooks is one of the leading accounting solutions on the market. It has a wide range of tools and services to support businesses of all sizes and industries. If you hire a delivery team, for example, you can count on QuickBooks’ mileage tracker to help you monitor them.

Better yet, QuickBooks seamlessly connects with Shopify with top accounting integration apps like MyWorks. You can map key data fields to match your business needs and update your books in real time.

Key features

• Multi-channel support: Connects you with a variety of sales platforms including Amazon and eBay
• Inventory management: Tracks products, calculates the Cost of Goods Sold, and notifies you about low stock
• Sales tax automation: Calculates and applies levies on transactions according to local US regulations
• AI assistant: Answers questions about your financial activities and history

Pros

• Specialist plans for ecommerce businesses
• Comprehensive features
• Extensive customer support

Cons

• Slight learning curve due to system complexity
• Higher cost than some alternatives

Best for: 

Due to its robust inventory tools and multichannel support, QuickBooks is ideal for growing businesses selling across multiple platforms. There’s less risk of losing track of orders and stock with the extra oversight.

QuickBooks is also a good call for US-based stores struggling with tax due to its automation, built-in compliance, and advisory services.

2. Xero

If QuickBooks doesn’t suit your needs, Xero may be the alternative you’re looking for. The platform offers more basic, user-friendly features at a lower monthly cost.

Just like QuickBooks, Xero offers a comprehensive solution for ecommerce businesses. You can reconcile transactions, track cash flow, and manage billing all from the lowest-cost plan. But the standout feature is Xero’s unlimited users — anyone can expand their team without worrying about sharing logins or adding more accounts.

However, currently none of the integrations available for Xero and Shopify are accredited by Shopify.

Key features

• Inventory tracking: Monitors stock levels and get reports on what’s selling quickly
• Advanced reporting: Checks your financial performance and forecast cash flow
• Multi-currency support: Converts currencies for international sales and gives you reports on how the exchange rate affects finances

Pros

• User-friendly interface
• Unlimited team members
• Lower cost than some alternatives
• Choice of integrations

Cons

• Expense tracking not included in the main plan
• Only basic inventory management tools available

Best for: 

Xero’s trim feature set makes it the perfect choice for ecommerce stores with basic needs. There’s no risk of your team getting overwhelmed by all the different tools. 

Like QuickBooks, it’s also an ideal fit for growing teams due to its range of integrations and unlimited users. You can easily add whichever HR, payroll, or workforce management tools you need to support your people. If you oversee sales teams, you can also connect with a range of Customer Relationship Management (CRM) solutions, too.

3. NetSuite

NetSuite is an enterprise resource planning (ERP) platform that includes accounting, inventory, and commerce tools among its many features. You can integrate these with Shopify through NetSuite’s own connector tool.

Many accounting solutions focus on the US market but NetSuite is designed to be a global solution. Its features are available in over 100 countries and it supports all the most widely spoken languages including French, Portuguese, and Chinese.

While NetSuite’s accounting software integrates with Shopify, be aware that it offers its own ecommerce platform called SuiteCommerce. Most of its tools are designed with this feature in mind rather than Shopify sites. 

Key features

• Global tax management: Calculates taxes in over 110 countries and generates reports for each foreign subsidiary
• Inventory management: Tracks stock across multiple locations and automates and predicts the best times to reorder products
• CRM integration: Connects to a native CRM solution with case management and a customer portal

Pros

• Comprehensive software solution
• Robust inventory features
• International availability
• Support for over 15 languages

Cons

• Complex pricing structure
• Higher setup and subscription costs than most alternatives
• Features too extensive for small businesses

Best for: 

NetSuite’s comprehensive range of features makes it ideally suited to enterprise-level organizations with retail operations. You can access a full suite of ecommerce, CRM, and marketing features in one place, meaning you can scale your operations without adding more software to your tech stack.

4. Zoho Books

If NetSuite is too complex for your needs, you might consider a more low-key option like Zoho Books. This platform also offers a suite of accounting, CRM, and payroll features, just for small to medium businesses.

Zoho Books offers users a Shopify accounting automation tool called Zoho Flow to manage data syncs. You can use this to connect your Shopify store and manage bank reconciliations and inventory levels. However, Zoho Flow isn’t a native Shopify integration so you have to manage tasks in a separate window rather than from your store’s backend.

Key features

• Vendor management: Lets you invite vendors onto your account and manage contracts via the platform
• Team collaboration: Gives administrators the ability to assign tasks to users and lock sensitive documents and reports
• Multi-channel management: Allows you to connect with a range of sales channels including Etsy and Amazon and manage them via Zoho Flow

Pros

• Lower cost than some alternatives
• Flexible pricing structure
• User-friendly interface
• Native CRM and payroll integration

Cons

• Standalone integration tool
• Shopify connections only available in the higher-cost plans
• Lacks advanced accounting features
• Restrictive user limits

Best for: 

Zoho Books is designed with solopreneurs and small businesses in mind. As you get started, you can access the essential features for free and keep upgrading as you grow. You can connect your Shopify store once you take more sales and handling transactions manually is no longer practical.

5. FreshBooks

FreshBooks is similar to Zoho in that it offers a range of basic features for small to medium businesses. The main difference is that FreshBooks is geared toward service-based industries whereas Zoho has more features specifically for ecommerce.

Aside from the basic accounting features, FreshBooks offers advanced invoicing, project tracking, and client management tools. You can push this data into your Shopify store with the right integration.

Similarly to other accounting software, FreshBooks doesn’t come with a dedicated Shopify sync. As FreshBooks is a less popular accounting platform, integration options are more limited. Currently there is only one syncing tool listed on the Shopify App Store.

Key features

• Payment processing: Lets you accept payments over the phone and manage subscription-based billing
• Invoicing: Automatically creates custom invoices for customers and clients 
• Reporting: Generates a range of reports including profit and loss, expense, and tax summaries

Pros

• Affordable pricing
• User-friendly interface
• Multi-currency support

Cons

• Fewer Shopify integrations than more popular alternatives
• Extra fees to add team members
• Limited customization options

Best for: 

Due to its focus on invoicing and client management, FreshBooks is best for service-based businesses that sell products on the side. Think hair stylists offering beauty products or education companies with their own textbooks.

Key features to look for in Shopify accounting software

Now we’ve compared the Shopify accounting software, here are some tips on how to choose between them.

The key idea to bear in mind is that Shopify can’t directly integrate with accounting software on its own. You need an ecommerce accounting integration tool like MyWorks to connect the platforms and seamlessly share data.

That’s why looking for Shopify accounting software isn’t just a straightforward comparison. To find the right one, you must consider how well they integrate with your store.

Here are the key concerns:

Features

Does the software include all the essential features? More importantly, are there plans tailored for ecommerce stores and specifically Shopify? Otherwise, you’ll find yourself adapting your processes to fit the tools instead of the other way around.

When using the Shopify integration tool, do you still get the full value of these features? One major concern is whether the sync updates automatically in real time. If the data isn’t reliable, neither is the software.

Customization

Are there plenty of settings and filters to tailor the accounting software to your workflow? For example, truly great software lets you generate custom reports and visualize them to get insights into your financial performance.

Again, consider whether the ecommerce accounting gives you the same level of customization. The best ones let you adjust how data is synced and managed.

User experience

Is the software quick to learn and easy to fit around your existing workflow? Accounting solutions should improve your efficiency and accuracy, not add complexity to your processes.

The same applies to the integration. If you have to keep manually transferring data, for instance, you won’t save much time using the software.

Total costs

Do all the software and integration subscriptions fit within your budget? Make sure there are no hidden fees that will drive the cost up for services like onboarding or adding team members.

If you’re just starting out, check whether there’s a free, basic plan you can use until you’re ready to expand. For example, MyWorks offers a forever free plan.

Scalability

Can you upgrade your plan to access more advanced features as you grow without significantly increasing your subscription costs? Also, consider whether you get the same value from the higher-tier accounting software and integration plans.

Integrations

Are there reliable Shopify accounting software integrations to connect all your tools? Do you have a choice of apps? Look for options that are Built for Shopify, like MyWorks, to ensure they fit seamlessly into the Shopify ecosystem.

‘Built for Shopify’ is an accolade given to apps that consistently meet Shopify’s highest standards. Seeing this badge signals that the integration is a dependable choice.

Accounting software your Shopify store can bank on

The accounting software you should choose depends on your specific requirements. While QuickBooks and Xero cover most use cases, some smaller businesses may prefer FreshBooks and enterprises might find NetSuite is best for their needs.

But when it comes to Shopify accounting, your software is only as good as its integrations. Sync tools decide how much functionality you get out of the platform. If they’re competitively priced, they help you keep costs low and manageable.

MyWorks understands this, which is why we aim to keep our Shopify accounting integrations flexible and affordable. When you connect to either QuickBooks Online or Desktop, you get full control over how you map your data like orders, customers and products. If you’re just starting up, we let you get the basics for free and upgrade when you’re ready.