5 Best Shopify Accounting Reporting Tools in 2025 [w/ Feature Comparison Table]

Are you struggling to manage your Shopify store’s finances? Discover the top accounting reporting tools that can simplify your financial management and boost your e-commerce success. This comprehensive guide will walk you through the best options available in 2025, helping you choose the perfect solution for your Shopify business.

Feature Comparison Table

Feature	FreshBooks	ZohoBooks	Xero	QuickBooks Online	Wave
Row Limits / Export Limits	Unlimited	Unlimited	Unlimited	Unlimited	Unlimited
Data Sources	Shopify, banks, payment gateways	Shopify, banks, payment gateways, 40+ apps	Shopify, banks, 800+ integrations	Shopify, banks, 650+ apps	Shopify, banks, payment gateways
Builder License Cost	$15-$55/month	$15-$70/month	$12-$65/month	$30-$200/month	Free (core accounting)
Viewer License Cost	Included in plans	$2/user/month	Unlimited users	$4-$10/user/month	Free
AI Functionality	AI-powered expense categorization	AI-powered data entry	AI-powered bank reconciliation	AI-powered insights and forecasting	Limited AI features
Refresh frequency	Real-time	Real-time	Real-time	Real-time	Daily
Alerts	Yes	Yes	Yes	Yes	Limited
Security	256-bit SSL encryption	256-bit SSL encryption	256-bit SSL encryption	128-bit SSL encryption	256-bit SSL encryption

#1 FreshBooks: Comprehensive Accounting for Shopify Stores

FreshBooks offers a robust accounting solution tailored for Shopify users, providing seamless integration and powerful reporting capabilities. Its user-friendly interface and e-commerce-specific features make it an excellent choice for Shopify merchants of all sizes.

Highlights of FreshBooks

• Real-time syncing with Shopify
• Customizable financial reports

Pros

• FreshBooks offers a clean, easy-to-navigate dashboard that simplifies accounting tasks for non-experts.
• Built-in time tracking helps service-based Shopify businesses accurately bill clients and manage project profitability.

Cons

• The lower-tier plans restrict the number of billable clients, which may be problematic for growing businesses.
• Some users report that the mobile app lacks full functionality compared to the desktop version.

Pricing

FreshBooks offers the following plan:

• Lite: $19/month
• Plus: $33/month
• Premium: $60/month
• Select: Custom pricing

Support

• Self-serve support available 24/7 through help center and chatbot
• Email support
• Phone support (for specific regions)
• Live chat (for specific regions)

#2 Zoho Books: Advanced Financial Management for Shopify

ZohoBooks offers a comprehensive suite of accounting tools that integrate seamlessly with Shopify, providing advanced reporting and financial management capabilities for e-commerce businesses.

Highlights of ZohoBooks

• Multi-currency support
• Automated bank feeds

Pros

• ZohoBooks connects with numerous third-party apps, enhancing its functionality for Shopify users.
• Users can create professional, branded invoices tailored to their Shopify store’s aesthetic.

Cons

• Some users find the interface less intuitive compared to other options, requiring more time to master.
• ZohoBooks offers fewer built-in payment gateway options compared to some competitors.

Pricing

ZohoBooks offers the following plans:

• Free plan available for businesses earning under $50K USD annually
• Standard: $15/month billed annually
• Professional: $40/month billed annually
• Premium: $60/month billed annually
• Elite: $120/month billed annually
• Ultimate: $240/month billed annually

Customer Support

• Classic Support (Free): Email support with 8 hour response time, available 24/5
• Premium Support: Email, live chat, phone, community forums, remote assistance. 3 hour response time, 24/5 availability. Costs 20% of license fee.
• Enterprise Support: Same channels as Premium, but with 1 hour response time and 24/7 availability. Costs 25% of license fee.

#3 Xero: Cloud-Based Accounting Solution for Shopify

Xero provides a powerful, cloud-based accounting platform that integrates well with Shopify, offering real-time financial insights and automated reporting for e-commerce businesses.

Highlights of Xero

• Unlimited users on all plans
• Inventory tracking

Pros

• Xero’s smart reconciliation features save time and reduce errors in matching Shopify transactions with bank statements.
• As your Shopify business grows, Xero can easily accommodate increased transaction volumes and more complex accounting needs.

Cons

• Some advanced reporting features are only available in higher-tier plans.
• Payroll features are not as robust as some competitors, which may be an issue for larger Shopify businesses.

Pricing

Xero offers the following pricing tiers:

• Early: $15/month
• Growing: $42/month
• Established: $78/month

Customer Support

• Free unlimited online support for subscribers
• No inbound phone support, but can request callback
• Community forums available

#4 QuickBooks Online: Industry-Standard Accounting for Shopify

QuickBooks Online offers robust accounting features and seamless integration with Shopify, making it a popular choice for e-commerce businesses of all sizes.

Highlights of QuickBooks Online

• Advanced inventory management
• Comprehensive tax support

Pros

• QuickBooks is widely used, making it easier to collaborate with accountants and financial advisors.
• QuickBooks Online offers a wide range of customizable reports tailored for e-commerce businesses.

Cons

• QuickBooks Online can be expensive for small Shopify stores, especially when additional users are needed.
• The wealth of features can be intimidating for those new to accounting software.

Pricing

QuickBooks Online has the following pricing tiers:

• Simple Start: $35/month
• Essentials: $65/month
• Plus: $99/month
• Advanced: $235/month

Customer Support

• Help articles and chatbot available 24/7
• Live chat and phone support available during business hours
• Advanced plan includes 24/7 support

#5 Wave: Free Accounting Solution for Small Shopify Stores

Wave provides a free, cloud-based accounting platform that integrates with Shopify, offering basic reporting and financial management tools ideal for small e-commerce businesses.

Highlights of Wave

• Forever free plan
• Unlimited income and expense tracking

Pros

• The core accounting features are free, making it an excellent option for Shopify startups and small businesses.
• Wave’s clean, intuitive design makes it easy for non-accountants to manage their finances.

Cons

• Some advanced features found in paid solutions are not available in Wave.
• Lack of built-in inventory management can be a drawback for product-based Shopify stores.

Pricing

Wave’s core accounting features are free. Wave Pro is offered for $16/month or $170/year.

Customer Support

• Help center and chatbot available 24/7 for all users
• Email and live chat support Monday-Friday 9am-4:45pm ET for paid users
• No phone support

Streamline Your Shopify Accounting with the Right Tools

Choosing the right accounting reporting tool can significantly improve your Shopify store’s financial management. Consider your specific needs, budget, and growth plans when selecting a solution.

To further enhance your reporting capabilities, consider integrating Coefficient with your chosen accounting tool for advanced data analytics and visualization.

Ready to take your Shopify reporting to the next level?

Get started with Coefficient today.

Further Reading

• How to Export Shopify to Excel: Shopify Microsoft Excel Integration
• Shopify Sales Dashboard: Visualize Store Metrics in Google Sheets
• How to Export Shopify Data
• Shopify Integration for Google Sheets
• Shopify Integration for Excel
• How to Connect Shopify to Salesforce? Top 3 Methods
• How to integrate Shopify to Snowflake? 3 Simple ways explained
• Shopify Order Dashboard Template for Spreadsheets

Frequently Asked Questions

Can you use Shopify as accounting software?

While Shopify provides basic financial reporting, it’s not designed to be a full-fledged accounting solution. For comprehensive accounting, it’s recommended to integrate Shopify with dedicated accounting software like those mentioned above. Coefficient can help streamline this integration process, ensuring seamless data flow between your Shopify store and accounting tools.

Can I do bookkeeping in Shopify?

Shopify offers basic bookkeeping features, but for more complex financial management, it’s best to use specialized accounting software. These tools can integrate with Shopify to provide more robust bookkeeping capabilities. Coefficient can enhance this integration by providing advanced data syncing and reporting features.

Does Shopify integrate with Sage accounting?

Yes, Shopify can integrate with Sage accounting using third-party apps or tools. This integration allows for the flow of accounting data from Shopify to Sage. Coefficient can further improve this integration by providing real-time data syncing and custom report building capabilities.

Does FreshBooks integrate with Shopify?

Yes, FreshBooks offers seamless integration with Shopify. This integration allows for automatic syncing of sales data, expenses, and other financial information. Coefficient can enhance this integration by providing additional data analysis and visualization tools, helping you gain deeper insights from your Shopify and FreshBooks data.