The Best Shopify Accounting Software

You’ve mastered Shopify, your sales are on the rise, and it seems your ecommerce venture is flourishing… but, you’re making most of these assumptions based on the balance in your bank account.

The only way to actually be certain if your Shopify store is making a profit is accurate Shopify accounting.

This is why you’re exploring “the best accounting software for Shopify merchants”, or something along those lines. You know it’s time to get insight into your business’s cash flow, and build and regularly review a Profit and Loss Statement (P&L) and Balance Sheet.

Or, maybe your CPA strongly suggested tidying up your accounts for tax filing.

Regardless of your motivation, you’ve come to the right place. This article will guide you through the best accounting software options for Shopify merchants. We’ve consulted with specialized ecommerce accountants and bookkeepers for their insights, so you can say that these tools are “accountant approved”.

Integrate Shopify and your accounting software for accurate accounting

A2X auto-categorizes your Shopify sales, fees, taxes, and more into accurate summaries that make reconciliation in your general ledger a breeze.

Try A2X today
Shopify integration (no GL)


What is the best accounting software for Shopify merchants?

There are so many accounting software options available for Shopify merchants. And, because every Shopify business is different, there’s no “absolute best” solution.

So, how do you find an accounting software solution that aligns perfectly with your Shopify store’s specific requirements?

We’ll review the following popular accounting software solutions for Shopify merchants (in no particular order):

  • QuickBooks Online
  • Xero
  • Sage
  • NetSuite

When assessing each option, think about your Shopify store’s unique needs and how well a solution could address them.

For example, you might want to consider if the accounting software will support:

  • The region(s) where you operate
  • Your expected business growth
  • Integrations with other ecommerce applications (e.g., inventory management tools)
  • Multi-currency
  • Sales tax management
  • User-friendliness
  • Financial reporting
  • Integrations with payment gateways
  • Any necessary customization

Perhaps most importantly, think about how you’ll get Shopify sales and transaction data into your chosen accounting software.

Most accounting software solutions will require an additional app or tool to integrate with Shopify so you can pull that data into your accounting.

Fortunately, A2X is an integration tool designed to get Shopify transaction data into accounting software and make Shopify bookkeeping easy – and, A2X will integrate with every accounting software solution on this list.

A visualization of A2X pulling Shopify transaction data into accounting software

QuickBooks Online for Shopify merchants

If you’re based in North America, QuickBooks Online by Intuit might already be familiar to you. It’s the accounting solution with the most small business customers in the United States and Canada.

QuickBooks Online (QBO) is highly regarded by many Shopify merchants and specialized ecommerce accountants for its comprehensive accounting features, security, and its ecosystem of third-party apps, including A2X.

A computer screen with an example of the QuickBooks Online dashboard

QuickBooks Online’s top benefits for Shopify merchants

  • Seamless Shopify integrations: You might have noticed that QuickBooks Online offers an integration to Shopify through its connector app. That said, the connector app is only well suited to smaller merchants with low order volumes. If you’re a larger merchant with more complex accounting needs, such as selling across multiple channels, payment gateways, countries, or with large order volumes – a benefit of working with QuickBooks Online is that it integrates with tools like A2X for accurate and automated revenue reconciliation. With this integration, all your Shopify sales, fees, refunds, gift cards, and more are categorized into accurate summaries that reconcile perfectly in QuickBooks Online – saving you hours and increasing your financial visibility.

  • Inventory management: QuickBooks Online helps Shopify merchants stay on top of stock levels, Cost Of Goods Sold (COGS), and inventory valuation. It can be an effective tool for managing inventory, preventing stockouts, and optimizing product availability.

  • Automated sales tax handling: QuickBooks Online navigates the complexities of sales tax across different states and countries. It can help automate sales tax calculations, ensuring compliance and simplifying tax reporting for your Shopify store.

  • Advanced reporting and analytics: With QuickBooks Online, you can get insights into your financial health and sales trends. Their reporting features are essential for Shopify merchants looking to optimize their business strategy based on reliable data.


“QuickBooks Online is perfectly suited for a Shopify merchant… it’s easy to use, facilitates communication between clients and accounting partners, and has most of the features a Shopify merchant would need. Where it doesn’t, it integrates with an ecosystem of amazing 3rd party applications.”

– Teresa Slack, founder of Financly, ecommerce bookkeeping experts

QuickBooks Online plan recommendations for ecommerce

QuickBooks Online provides a range of plans in various currencies. The availability of these plans can differ by country.

A2X can integrate with every QuickBooks Online plan. However, to manage transactions in different currencies with A2X, the Essentials package or a higher one is required.

The Plus plan is advised for Shopify merchants because of its superior inventory management and profitability assessment capabilities. For those located in the United States looking to begin with QuickBooks Online, consider utilizing A2X’s special promotional pricing for QuickBooks Online.

Xero for Shopify merchants

If you’re in the United Kingdom, Australia, or New Zealand, Xero might be a familiar name. It’s the leading cloud accounting software in these regions since its inception in 2006. Designed from the ground up for the cloud, Xero enables extensive integrations to streamline accounting and enhance accuracy.

Shopify merchants and ecommerce accountants trust Xero for its comprehensive features and seamless user experience. Its prowess in managing multiple currencies is especially valuable for international merchants.

Hands holding a tablet with the Xero dashboard on the screen

Xero’s standout features for Shopify merchants

  • Ecommerce platform integrations: Similarly to QuickBooks Online, Xero offers an integration with Shopify that is well suited for small merchants with little accounting complexity. But for larger merchants selling products across multiple channels, payment gateways, and countries, a benefit of working with Xero is that it seamlessly integrates with A2X to simplify revenue reconciliation and to ensure your Shopify sales, fees, and other transaction data are accurately reflected on your financial statements for visibility and tax.
  • Multi-currency support: Xero’s capability to handle multiple currencies is crucial for international Shopify merchants, automatically updating exchange rates for hassle-free foreign transaction management.
  • Detailed financial reporting: Xero’s reporting tools offer deep insights into your financial health, with comprehensive analyses including Profit and Loss Statements and cash flow assessments.
  • Inventory management: While not as advanced as specialized systems, Xero provides essential inventory tracking to help merchants manage stock levels and assess product performance.
  • Cloud-based access: Xero allows merchants to access their financial data anywhere, enabling seamless updates, integrations, and timely business decisions. Although this is similar to other cloud accounting solutions, Xero was natively built in the cloud, which means that it is inherently designed to support the flexibility that ecommerce businesses often require.

“We think Xero is the best general ledger solution for international Shopify merchants, especially those that deal with foreign currency and sell into the US market.”

– Jason Macdonald, Partner at Intrepid Advisory

Xero plan recommendations for ecommerce

Xero offers a variety of plans, available in most currencies. The availability of plan options can differ by country.

A2X integrates with all Xero plans. However, for merchants intending to handle transactions in multiple currencies with A2X, you’ll need the Premium package (or higher).

For Shopify sellers who require global transactions, the Established package will likely work best due to its comprehensive multi-currency functionality.

Sage for Shopify merchants

In the UK, Sage is a well-recognized name, offering robust desktop and cloud accounting solutions since 1981. Sage Business Cloud Accounting is particularly suited for Shopify merchants seeking a comprehensive cloud-based accounting tool.

An example of the Sage accounting dashboard

Key Sage features for Shopify merchants

  • Shopify integration: Sage Business Cloud Accounting seamlessly integrates with Shopify through tools like A2X, enabling accurate reconciliation of sales, fees, taxes, and other transactions – saving you hours and increasing the accuracy of your books.
  • Inventory management: Offers tools for efficient stock management with real-time data and inventory reports, alerting you to low stock levels.
  • Multi-currency capabilities: Supports transactions in various currencies, essential for merchants dealing internationally.

Sage plan recommendations for ecommerce

A2X integrates Shopify and Sage, and specifically will connect to the Sage Business Cloud UK (Plus plan) and Sage One UK (Plus plan).

The Sage Business Cloud Accounting Plus plan (£36/month) provides a good balance of features and affordability for Shopify merchants.

NetSuite for Shopify merchants

For Shopify merchants at scale, NetSuite provides a comprehensive ERP solution, ideal for large ecommerce businesses that require intricate accounting, inventory, operations, and financial management.

An example of what the NetSuite dashboard looks like

NetSuite’s offerings for Shopify merchants:

  • Comprehensive ERP and CRM: Supports larger Shopify merchants with a suite of tools to manage their business lifecycle in one platform.
  • Advanced inventory management: Detailed tracking and real-time stock level insights are pivotal for merchants with extensive inventory.
  • Global business management: Features support for multi-currency, multi-language, and multi-subsidiary operations, crucial for international scalability.

NetSuite plan recommendations for ecommerce

NetSuite’s pricing is tailored to the specific requirements of each business, usually beginning from several thousand dollars annually.

We suggest that larger Shopify retailers or businesses with intricate multinational activities reach out to NetSuite directly to explore their options.

Integrating Shopify with your accounting software via A2X

A2X makes reconciling your Shopify payout data in QuickBooks Online, Xero, Sage, or NetSuite a breeze. Every Shopify transaction – sales, fees, taxes, refunds, gift cards, and more – is categorized into accurate summaries that reconcile perfectly with deposits in your accounting software.

Leading merchants, accountants, and bookkeepers trust A2X to save hours on their bookkeeping, accurately track their taxes and COGS, increase the quality of their P&L, and gain true financial visibility.

Whether you’re selling on Shopify only, or across multiple channels, in different countries, A2X has the robust functionality you need to manage any level of accounting complexity.

“Clients who use A2X are reconciling their books faster, have up-to-date information, and have what they need to make good, timely business decisions.”

– Jay Kimelman, President of High Rock Accounting

“We use A2X with our accounting and the process is seamless! A2X allows us to connect Shopify, Amazon, eBay and Walmart. Best application I’ve used for multiple storefronts.”

– Accounting Department, iRestore Hair Growth Systems

“We love using A2X because they help us reconcile the revenue data and post Cost of Goods Sold cleanly and easily. We’ve been using A2X since 2014. We love their team, they’re super responsive to our needs, and the support is amazing.”

– Patti Scharf, founder of Catching Clouds (now Acuity), first specialized ecommerce accounting practice in the US

Try A2X for free today!

Selecting the right accounting software for your Shopify store

Choosing the appropriate software is vital for accurate books and financial visibility. If in doubt, consult with an expert ecommerce accountant who can guide you to the best solution for your Shopify business.

Find an expert ecommerce accountant on the A2X Partner Directory.

Integrate Shopify and your accounting software for accurate accounting

A2X auto-categorizes your Shopify sales, fees, taxes, and more into accurate summaries that make reconciliation in your general ledger a breeze.

Try A2X today
Shopify integration (no GL)

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