Best Accounting Software for Shopify

Accounting software can be a lifesaver for anyone running a Shopify store. It helps you keep track of your income, manage expenses, and stay clear on your finances without the hassle of manual data entry.

In a ecommerce setting, having a reliable accounting tool means you can concentrate more on selling and less on spreadsheets.

What It Is

In simple terms, accounting software is a digital tool that helps you record and organize financial transactions in your business.

It automates tasks like categorizing expenses, sending invoices to customers, and even generating reports that show how your business is performing overall. When paired with an online store like Shopify, the software automatically collects data from your sales, refunds, shipping costs, and taxes.

Once everything is connected, transactions are added to your books automatically.

This integration means you don’t have to copy and paste sales info from Shopify into your accounting system. It also minimizes the chance of mistakes because the system consistently matches your store data with your records.

Key Aspects to Consider

When you are looking for an accounting solution that works well with Shopify, keep these important points in mind:

• Integration with Shopify: Some options are designed to work closely with the Shopify platform. This ensures a direct flow of data and saves you time.
• Pricing Plans: Costs can vary widely. Some providers offer free versions with limited features, while others charge on a monthly or yearly basis. Make sure you know your budget and growth plans to make the right choice.
• User-Friendliness: If you are not an accounting expert, you might prefer a dashboard with simpler tools. This makes everyday tasks like invoicing, reconciling bank accounts, or viewing sales summaries easier.
• Scalability: As your Shopify business expands, your bookkeeping needs may become more complex. Choose software that can handle increasing transaction volumes, more product lines, and additional team members.
• Reporting Tools: Basic bookkeeping is helpful, but custom reports that show profit and loss, cash flow, and inventory costs are essential for making informed decisions about your store.
• Customer Support: If you run into issues, you will want prompt and helpful assistance. Look for vendors who offer support through chat, email, or phone.

The 10 Best Accounting Software for Shopify

1. Xero [Best for growing businesses]

Xero is often praised for its intuitive interface, which many non-accountants appreciate.

It connects with Shopify through third-party apps, pulling in all your sales data so you can keep your finances in check. Xero’s clean dashboard keeps track of your invoices, bills, and bank accounts in real-time so you always have a clear overview of your financial status.

PROS

• User-friendly layout with clear navigation
• Strong reporting features to analyze cash flow and profit
• Smooth connection with many payment gateways and other ecommerce tools
• Automatic data syncing that saves time on manual entry

CONS

• Lower-tier plan limits the number of invoices and bills that can be processed
• Some users might need guidance when setting up extra features for advanced needs
• Prices increase as your business scales

Best for: Small to medium-sized Shopify sellers who plan to grow quickly and need an easy-to-use accounting solution.

Price: Plans start at $15/month for the Early option, then $42/month for the Growing tier, and $78/month for Established.

2. FreshBooks [Best for service-focused sellers]

FreshBooks is known for its sleek, approachable design that simplifies basic bookkeeping and invoicing.

It supports Shopify primarily through integrations that sync data like sales, taxes, and listings. Entrepreneurs who also offer services such as consulting or freelance work alongside ecommerce find FreshBooks helpful with its straightforward time tracking and invoice management.

PROS

• Very clean interface suitable for non-accountants
• Automated invoicing and recurring billing
• Mobile app available for access on the go
• Reliable customer support and resources

CONS

• Basic plans limit the number of clients that can be invoiced
• Advanced features like complex inventory tracking are limited
• Extra fees for adding multiple team members

Best for: Freelancers or small Shopify store owners who also provide services and need a simple way to bill clients.

Price: Plans start at $19/month for the Lite plan, $33/month for Plus, and $60/month for Premium.

3. Zoho Books [Best for multi-channel sellers with tight budgets]

Zoho Books offers a variety of accounting features at competitive prices. If your business makes less than $50,000 in annual revenue, there is even a free version available.

The software handles invoicing, expense tracking, and various other tasks to keep you organized. It can integrate with Shopify through Zoho Flow, though that may involve an extra fee.

PROS

• Generous free tier for new or smaller businesses
• Good automation for recurring invoices and expense categorization
• Built-in inventory management for product-based businesses
• Mobile app available for both iOS and Android

CONS

• Certain features require higher plans or additional fees
• Shopify integrations are handled through Zoho Flow, which can add complexity
• Not as widely used among external accountants compared to some well-known tools

Best for: Budget-conscious Shopify entrepreneurs selling across multiple channels who need basic accounting with room to upgrade later.

Price: Paid plans start at $20/month (Standard), $50/month (Professional), and $70/month (Premium).

4. A2X [Best for detailed ecommerce data]

A2X is a specialized tool rather than a full accounting software package. It pulls data from Shopify and sends it accurately into platforms like Xero, QuickBooks Online, or Sage.

It is designed for ecommerce, so if you handle many orders, refunds, and complex sales tax requirements, A2X can help sort these details while reducing the risk of mistakes.

PROS

• Automatically matches and categorizes Shopify transactions
• Assists with intricate sales tax calculations
• Supports major ecommerce channels like Amazon and Etsy too
• Provides a detailed breakdown of transaction fees and payouts

CONS

• Requires a separate accounting software for full bookkeeping
• The monthly fee can be high for very large order volumes
• Fewer standalone accounting features

Best for: Shopify store owners who already use programs like Xero or QuickBooks and need a specialized tool that handles detailed ecommerce transactions.

Price: Starts at $29/month for up to 200 orders, ranging up to $115/month for 5,000 orders.

5. Bench [Best for hands-off bookkeeping assistance]

Bench provides bookkeeping services combined with software, making it a good option if you want extra support. Instead of just offering a tool, Bench pairs technology with a dedicated team of bookkeepers who handle categorizing transactions, reconciling accounts, and generating monthly financial statements.

It integrates with Shopify to pull data automatically, but keep in mind that this is primarily a service-based solution.

PROS

• A team of professional bookkeepers handles most of the work
• Easy-to-read monthly reports delivered directly
• Communication managed through a user-friendly dashboard
• Ideal for those who prefer not to manage bookkeeping themselves

CONS

• Can be more expensive than self-managed accounting software
• Less flexibility if you enjoy handling tasks and customizing the system
• Additional fees may apply for advanced services like tax filing

Best for: Shopify merchants who want limited involvement in daily bookkeeping and prefer professionals to handle most financial tasks.

Price: Plans typically start around $299/month, though exact costs depend on your monthly expenses and service level.

6. Sage 50 [Best for larger operations needing advanced reporting]

Sage 50 is a robust system offering advanced features beyond basic bookkeeping. It is a desktop-based software that connects to the cloud for data backups and certain online functions. Its strong points include detailed forecasting tools, job costing analyses, and solid inventory management.

You might find it less straightforward for a direct Shopify connection, but it remains a valid option if you have a more complex setup and can manage additional integration steps.

PROS

• Detailed reports for analyzing profits, inventory, and job costs
• AI-assisted error checking helps reduce mistakes
• Options for multiple users and scaling
• Well-suited for companies handling large stock levels and numerous projects

CONS

• Higher cost compared to many cloud-based alternatives
• Desktop-first design might seem outdated if you prefer purely online solutions
• Lacks an official direct integration with Shopify

Best for: Established Shopify businesses with complex financial activities—such as multiple warehouses or larger teams—seeking deeper financial insights.

Price: Starts at $625/year for the Pro version (one user). Premium and Quantum versions exceed $1,000/year and are designed for multi-user environments.

7. Bookkeep [Best for automated nightly reconciliations]

Bookkeep automates the process of posting sales summaries from Shopify to your general ledger. It specializes in end-of-day reconciliation, which is valuable if you run a busy store with many transactions.

With Bookkeep, you can set rules for how revenue, refunds, fees, and taxes are categorized. The software then updates your accounting platform, such as QuickBooks Online or Xero, with accurate entries every night.

PROS

• Focuses on daily reconciliation for improved day-to-day accuracy
• Supports multiple payment methods, including Shopify Payments and PayPal
• Straightforward rules engine for custom category mapping
• Significantly reduces manual bookkeeping tasks

CONS

• Requires separate primary accounting software
• Not a complete accounting solution on its own
• Pricing may increase if more sales channels or higher transaction volumes are added

Best for: Shopify store owners who want to automate daily reconciliation without manually importing every transaction.

Price: Plans often start at around $39/month, with costs depending on transaction volume and platform connections.

8. QuickBooks Online [Best for mainstream familiarity]

QuickBooks Online is widely recognized as a top choice for small businesses. It links with Shopify through third-party apps, automatically importing sales, refunds, and payouts into your accounts. QuickBooks offers features such as automatic expense categorization, invoice creation, and sales tax tracking.

Multiple plan tiers provide options for inventory tracking, advanced analytics, and automation.

PROS

• Widely used among accountants, making it easier to find external help
• Automatic invoice reminders and expense entry via photos or email
• A large number of integrations with other software and apps
• A trusted brand with regular updates

CONS

• The feature set can be overwhelming for beginners
• Some useful functions like inventory tracking are only available in higher tiers
• Costs rise with more advanced plans

Best for: Shopify merchants looking for a well-known, reliable accounting tool with many integration options and widespread accountant support.

Price: Starts at $35/month for Simple Start. Essentials is $65/month, Plus is $99/month, and Advanced is $235/month.

9. Patriot [Best for combining payroll and accounting]

Patriot is an online solution that offers both accounting and payroll on one platform. It includes basic features like invoice creation and payment tracking, along with a payroll system for part-time or full-time employees.

While Patriot does not offer a direct Shopify integration, you can connect it through third-party services or by importing your Shopify sales data via CSV.

PROS

• Clean, user-friendly design
• Strong built-in payroll features for businesses with employees
• An affordable option for small businesses seeking an all-in-one solution
• Customizable invoice templates and some automation features

CONS

• Does not have a direct built-in Shopify integration
• May not scale well for very high transaction volumes
• Offers fewer advanced analytics or inventory tools compared to larger competitors

Best for: Small to medium Shopify stores with a few employees that value having payroll and accounting in one place.

Price: Basic accounting plans start at around $20/month, plus additional fees if you add the payroll module.

10. Wave [Best for absolute beginners on a tight budget]

Wave provides free basic accounting, which makes it appealing if you are just getting started with Shopify and have a limited budget.

You can manage unlimited invoicing, track expenses, and view the overall performance of your store. If you need extra features, there are paid add-ons for payment processing and payroll.

PROS

• The free plan covers unlimited invoices, expenses, and basic reporting
• Fairly intuitive interface
• Invoicing, bill tracking, and receipt scanning all in one place
• A good fit for new businesses or part-time ventures

CONS

• Lacks a direct Shopify integration, which means using manual or third-party data transfers
• Fewer advanced tools for inventory management or forecasting
• Paid services can add up if you require advanced features

Best for: Shopify solopreneurs and very small businesses with minimal inventory and a limited budget for accounting software.

Price: Basic functionality is free; additional services like payments and payroll incur extra costs (for example, $16/month for Pro features in certain regions).

Best Accounting Software for Shopify Comparison

This table provides a quick comparison of the top accounting software for Shopify sellers, highlighting what each is best suited for and its main distinguishing feature.

This table summarizes the key strengths of different accounting software solutions, helping Shopify store owners find the best fit based on their business needs.

Shopify Accounting Software FAQ

Having an accounting software integration with Shopify can simplify bookkeeping and financial management. Below are common questions about selecting and using these tools.

Why do I need accounting software for my Shopify store?

Managing finances manually can be time-consuming and error-prone. Accounting software automates sales tracking, expense categorization, and tax calculations, helping you maintain accurate records and make better financial decisions.

Which accounting software integrates directly with Shopify?

Options like Xero, QuickBooks Online, and A2X have seamless integrations, automatically syncing sales data from your Shopify store. Other software may require third-party apps to connect.

Can I use free accounting software for my Shopify business?

Yes, Wave offers free bookkeeping features, but it lacks direct Shopify integration. If you need automation, upgrading to a paid tool may be more efficient.

What’s the best option for beginners with no accounting experience?

FreshBooks and Wave are good choices for beginners due to their simple interfaces and intuitive features. QuickBooks Online also offers automation to reduce manual work.

Do I need separate accounting software if I already use Shopify’s built-in financial reports?

Shopify’s reports provide basic insights, but dedicated accounting software ensures full financial tracking, tax compliance, and structured bookkeeping necessary for growing businesses.

Which accounting tool is best for high-volume Shopify stores?

A2X is ideal for managing high transaction volumes because it accurately reconciles Shopify payouts and tax reporting. Sage 50 also works well for large-scale operations needing advanced financial insights.

How much does Shopify accounting software usually cost?

Prices range from free (Wave) to hundreds per month (Bench, Sage 50). Most cloud-based options, like Xero and QuickBooks Online, start at around $15–$35 per month, with higher-tier plans offering more features.

Can I switch accounting software later if my Shopify store grows?

Yes, most accounting software allows data export/import. Look for scalable options like Xero, QuickBooks, or Zoho Books that can adapt as your business expands.

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