E-commerce companies must effectively manage their finances, and the correct accounting software may make bookkeeping, tax compliance, and financial reporting easier. By 2025, e-commerce companies will need cutting-edge technologies that automate transactions, offer real-time information, and interface seamlessly with online retailers. The top 30 e-commerce accounting software in 2025 are listed here, along with an overview of their features and advantages.
Top 30 E-Commerce Accounting Software in 2025
1. QuickBooks Online
QuickBooks Online remains one of the leading cloud-based accounting solutions for e-commerce businesses. It offers automated invoicing, expense tracking, real-time reporting, and seamless integration with platforms like Shopify and WooCommerce.
2. Xero
Xero is a powerful accounting software designed for small to medium-sized businesses. It features automated bank reconciliation, multi-currency support, inventory management, and seamless integrations with leading e-commerce platforms.
3. Zoho Books
Zoho Books is an affordable and comprehensive accounting solution that includes invoicing, tax management, and inventory tracking. It integrates with payment gateways and e-commerce platforms to ensure smooth financial operations.
4. FreshBooks
FreshBooks is a user-friendly accounting solution ideal for freelancers and small e-commerce stores. It provides automated billing, expense tracking, and time management tools.
5. A2X
A2X automates e-commerce accounting by integrating with Shopify, Amazon, and eBay, ensuring accurate financial data syncing and reporting.
6. NetSuite
NetSuite is an enterprise-level cloud-based ERP solution that includes robust accounting tools, financial forecasting, and advanced reporting features for large e-commerce businesses.
7. Sage 50cloud
Sage 50cloud is a hybrid accounting solution that combines desktop functionality with cloud-based features, offering comprehensive financial tracking, invoicing, and tax compliance tools.
8. Wave Accounting
Wave Accounting is a free accounting tool with features like invoicing, expense tracking, and payroll management, making it ideal for small e-commerce businesses.
9. MYOB
MYOB provides powerful accounting and inventory management tools tailored for e-commerce businesses, with seamless integrations for online stores.
10. TallyPrime
TallyPrime (formerly Tally.ERP 9) is a widely used accounting solution with GST compliance, multi-currency support, and inventory management features for e-commerce businesses.
11. SAP Business One
SAP Business One is an ERP software that offers accounting, sales tracking, and financial reporting capabilities for medium to large e-commerce enterprises.
12. Microsoft Dynamics 365 Business Central
Microsoft Dynamics 365 is a cloud-based business management solution that integrates accounting, sales, and supply chain management for e-commerce businesses.
13. FreeAgent
FreeAgent is a cloud-based accounting software tailored for freelancers and small businesses, offering real-time tax tracking, invoicing, and reporting.
14. Kashoo
Kashoo simplifies small business accounting with AI-driven automation, invoicing, and bank reconciliation features.
15. OneUp
OneUp automates transaction categorization, inventory management, and accounting tasks for e-commerce businesses.
16. Brightpearl
Brightpearl is a retail-focused accounting and order management system that integrates with Shopify, BigCommerce, and WooCommerce.
17. Sellsy
Sellsy combines accounting, CRM, and invoicing tools, offering a streamlined solution for e-commerce financial management.
18. AccountEdge
AccountEdge provides powerful desktop-based accounting features, including payroll, invoicing, and inventory management.
19. Bench
Bench is a bookkeeping service that offers real-time financial data and automated transaction categorization for e-commerce businesses.
20. Plooto
Plooto automates accounts payable and receivable processes, improving cash flow management for e-commerce companies.
21. Patriot Accounting
Patriot Accounting is an affordable accounting tool that provides invoicing, expense tracking, and tax management features.
22. Synder
Synder specializes in automating financial transactions for e-commerce businesses, ensuring seamless accounting data synchronization.
23. Expensify
Expensify is an expense management tool that integrates with leading accounting software to streamline financial operations.
24. Sunrise
Sunrise offers free accounting tools for small businesses, including invoicing, expense tracking, and profit analysis.
25. ClearBooks
ClearBooks is a cloud-based accounting solution that provides automated invoicing, VAT tracking, and multi-currency support.
26. Tipalti
Tipalti is an automated global payment solution that helps e-commerce businesses streamline financial processes.
27. SlickPie
SlickPie is an easy-to-use accounting solution that offers automated billing and bank reconciliation.
28. ZarMoney
ZarMoney is a scalable cloud accounting platform with robust inventory tracking and invoicing features.
29. Melio
Melio is a payment management tool that enables e-commerce businesses to manage invoices and accounts payable efficiently.
30. Gusto
Gusto is a payroll and accounting software solution that integrates with various e-commerce platforms to streamline financial management.
Conclusion
In 2025, a company’s size, transaction volume, and integration requirements will all influence the choice of e-commerce accounting software. Whether choosing a user-friendly platform like Xero or an all-in-one ERP solution like NetSuite, these accounting tools assist companies in automation, compliance, and financial decision-making.