Top 10 Best Accounting Software for Ecommerce Businesses in 2025

Ecommerce accounting software is a specialized solution designed to manage and automate the unique financial tasks of online businesses. Unlike traditional accounting software, it is specifically built to handle the complexities of ecommerce, such as multi-channel sales, inventory management, tax compliance, and integrated payment processing. As ecommerce businesses grow, the volume of transactions, customer data, and financial intricacies increase, making it increasingly difficult for manual bookkeeping or generic accounting tools to keep up. Best ecommerce accounting software addresses these challenges, ensuring efficiency, accuracy, and scalability as businesses expand.

However, with various accounting software options available, each offering a unique set of features, pricing structures, and integrations, it can be overwhelming for ecommerce businesses to navigate the choices. This blog discusses a curated list of the top 10 accounting software for ecommerce businesses to help them make a well-informed decision based on their business size, industry, budget, and long-term goals. 

Best Ecommerce Accounting Software in 2025

Here is the list of tailored accounting software for ecommerce businesses designed to streamline operations, help with accurate reporting, and maintain compliance with tax regulations.

1. QuickBooks Online

QuickBooks Online is one of the leading choices for ecommerce businesses due to its comprehensive accounting solutions and adaptability. It offers robust support for various financial tasks, including automated processes and seamless integrations with major ecommerce platforms. QuickBooks online accounting software for ecommerce businesses helps manage finances with real-time data tracking and makes informed decisions. Its user-friendly design, continuous updates, and innovations ensure that ecommerce businesses can streamline financial operations and stay ahead of their accounting needs in an ever-evolving digital marketplace.

Key Features

• Real-Time Financial Tracking: Allows users to monitor their income, expenses, and overall financial status in real-time, providing a dynamic view of cash flow and transactions as they happen. 
• Automatic Bank and Credit Card Reconciliation: Automatically matches bank transactions to corresponding entries, reducing the chances of manual errors and ensuring accurate bookkeeping.
• Inventory Management: Offers detailed tracking of stock levels, product orders, and supplier management, ensuring that businesses maintain optimal inventory.
• Multi-Currency Support: Allows transactions in multiple currencies to help e-commerce businesses with an international customer base.
• Ecommerce Platform Integration: Integrates seamlessly with popular platforms like Shopify and WooCommerce, syncing sales and orders for a streamlined accounting process. 

Pros:

• Widely used with extensive features for ecommerce businesses.
• Easy integration with various ecommerce platforms (e.g., Shopify, Amazon).
• Strong reporting and tax compliance tools.
• Scalable as businesses grow.

 2. Xero

Xero is an essential cloud-based accounting software for ecommerce businesses. It is known for its powerful collaboration capabilities and intuitive interface. Xero helps ecommerce businesses simplify the financial management process and keep accounting automated and efficient.  With live synchronization and comprehensive reporting, Xero allows businesses to stay connected and updated on the financial health of their operations. Its adaptability for different-sized businesses ensures that it meets the needs of smaller e-commerce entrepreneurs and larger-scale operations and functions as a reliable accounting backbone for growth.

Key Features

• Live Dashboard with Cash Flow Updates: Displays a real-time overview of business finances, showing metrics such as income, expenses, and bank balances at a glance for easy monitoring.
• Bank Reconciliation: Simplifies the process by automatically importing bank statements and matching transactions, allowing quick reviews and approvals for accuracy.
• Expense Tracking: Offers an intuitive way to manage expenses through receipts and expense claims, which can be scanned and uploaded via mobile apps.
• Payroll Integration: Facilitates payroll management, allowing users to manage employee payments, deductions, and tax filings directly from the platform.
• Multi-Currency Transactions: Handles global sales seamlessly, updating exchange rates in real-time and providing accurate reports for multi-currency transactions.

Pros:

• Excellent multi-currency support for international ecommerce businesses.
• Robust reporting tools with customizable dashboards.
• Seamless integration with multiple ecommerce platforms and third-party apps.
• Unlimited users are included in all plans.

3. FreshBooks

FreshBooks is one of the best ecommerce accounting software tailored for small to mid-sized ecommerce businesses. Recognized for its intuitive design, FreshBooks simplifies the process of financial management and allows ecommerce businesses to focus on their core business. Its versatility helps with time-saving, automation, and detailed financial tracking, making it easy to manage day-to-day accounting activities. FreshBooks’ ability to integrate with various payment and ecommerce platforms further enhances its value as an all-in-one solution. It supports the need for agility and efficiency in the competitive ecommerce market.

Key Features

• Time Tracking and Project Management: Offers built-in time tracking for billing clients by tracking hours and project timelines for accurate invoicing.
• Mobile Expense Capture: Allows users to take photos of receipts and categorize expenses directly through a mobile app, simplifying expense management on the go.
• Automated Invoicing: Helps users to customize invoices with branding, set up automatic reminders for late payments, and receive notifications when an invoice is viewed.
• Integrated Payments: Supports receiving payments directly from invoices, allowing faster transactions and better cash flow.
• Multi-Device Sync: Ensures seamless transitions between desktop and mobile versions, allowing business owners to access data from anywhere.

Pros:

• Simple and intuitive, it is great for small ecommerce businesses.
• Excellent customer support and time-tracking features.
• Provides automatic expense tracking and invoicing.
• Integrates with various ecommerce platforms like Shopify and PayPal.

4. NetSuite by Oracle

NetSuite by Oracle is one of the top ecommerce accounting software for larger businesses that look for integrated financial and operational management. Its ERP platform combines advanced accounting, inventory control, and real-time business intelligence to meet the demands of complex enterprises. With extensive customization options and a scalable framework, NetSuite accommodates growing businesses that handle high volumes of transactions and data. Its advanced technology supports a holistic approach to ecommerce management by covering everything from accounting to CRM and ensures that businesses stay aligned with their strategic objectives.

Key Features

• Real-Time Business Analytics: Provides detailed dashboards and KPI tracking, allowing businesses to analyze data and gain insights into their financial and operational performance.
• Advanced Revenue Management: Automates revenue recognition based on various models, ensuring compliance with accounting standards and regulations.
• CRM and Inventory Integration: Links customer relationship management functions with inventory, offering a unified approach for sales, marketing, and fulfillment.
• Automated Accounts Payable/Receivable: Streamlines AP and AR functions by managing invoices, payments, and credits without manual entry, improving accuracy and efficiency.
• Robust Customization: Allows businesses to tailor workflows, reports, and processes to meet specific needs.

Pros:

• Highly scalable and ideal for large or growing ecommerce businesses.
• Comprehensive suite covering everything from accounting to ERP (Enterprise Resource Planning).
• Advanced reporting and financial management tools.
• Strong multi-currency and global tax compliance support.

5. Zoho Books

Zoho Books is an affordable, feature-rich accounting software designed for small to medium-sized ecommerce businesses. It offers end-to-end accounting capabilities, helping businesses easily manage their finances, tax compliance, and inventory. As an ecommerce accounting solution, Zoho Books seamlessly integrates with other Zoho applications and popular third-party ecommerce platforms, ensuring businesses can operate efficiently without switching between multiple systems. The simplicity and flexibility of Zoho Books make it a trusted choice for ecommerce businesses looking to streamline operations and maintain accurate, clear financial records.

Key Features

• Automated Workflows: Users can set up custom workflows that trigger specific actions (e.g., sending an invoice or email) based on business rules, enhancing operational efficiency.
• Real-Time Collaboration Tools: This tool supports collaboration among team members and accountants with different access levels to ensure secure data sharing.
• Comprehensive Tax Support: Provides automated tax calculations and compliance support for different regions, simplifying sales tax management.
• Inventory Management: Helps businesses manage stock levels, automate reorder points, and create detailed inventory reports.
• Multi-Currency Transactions: This department handles payments, expenses, and invoices in multiple currencies, adjusting for live exchange rates and conversions.

Pros:

• Affordable, feature-rich solution for small to medium-sized ecommerce businesses.
• Strong integration with other Zoho apps and third-party platforms like Shopify.
• Automated workflows and detailed reporting.
• Excellent inventory management features.
  

7. Wave

Wave is a free and intuitive ecommerce accounting software for small businesses. It simplifies financial management by helping business owners track income and expenses and generate invoices while ensuring tax compliance. Wave enables efficient transaction processing and real-time financial reporting with seamless integration into payment platforms and bank accounts. Ideal for businesses on a budget, This accounting software for ecommerce companies provides essential tools for managing finances and a reliable solution for small ecommerce operations.

Key Features

• Free Accounting Tools: No monthly fees for core accounting features, making it ideal for small businesses on a budget.
• Invoice & Payment Management: Create and send professional invoices and receive online payments through integrated payment gateways.
• Receipts Scanning: Automatically capture and categorize receipts with mobile scanning, streamlining expense tracking.
• Bank Integration: Syncs directly with bank accounts to track real-time income and expenses.
• Financial Reporting: Generates key reports like balance sheets, profit and loss, and cash flow statements.

Pros:

• Completely free for core accounting features (ideal for startups).
• Easy-to-use interface with basic accounting tools.
• Good for small businesses with simple needs.
• Integrates with bank accounts and payment processors.

8. Sage Business Cloud Accounting

Sage Business Cloud Accounting is a comprehensive solution for small and growing ecommerce businesses. It offers tools for invoicing, cash flow management, and financial reporting designed to scale as businesses grow. Sage integrates seamlessly with ecommerce platforms and third-party tools, providing flexibility and efficiency. With its user-friendly interface and powerful features, Sage helps businesses manage finances, streamline operations, and maintain financial visibility. This makes it a perfect choice for ecommerce businesses looking for an adaptable and scalable accounting solution.

Key Features

• Cash Flow Management: Track cash flow easily, manage payments, and ensure timely invoicing to maintain financial health.
• Comprehensive Reporting: Provides real-time insights into your finances with various customizable reports.
• Tax Compliance: Supports VAT, sales tax, and other region-specific taxes, helping businesses stay compliant.
• Automation: Automates routine tasks like invoice creation, recurring payments, and reminders.
• Multi-User Access: Allows multiple users with customizable roles for better team collaboration and control.

Pros:

• Scalable and suitable for both small and growing businesses.
• Excellent cash flow management and invoicing tools.
• Strong multi-currency support and customizable reports.
• Integrates with different third-party apps and ecommerce platforms.

8. MYOB

MYOB is an accounting software designed for small to medium-sized ecommerce businesses. It automates key financial tasks such as payroll, tax compliance, and inventory management, saving time and reducing manual effort. With seamless integration capabilities, MYOB helps businesses streamline operations and maintain accurate financial records. This allows businesses to emphasize growth and strategic decision-making while ensuring critical financial processes are handled efficiently and compliantly. MYOB is a reliable solution for ecommerce businesses looking to simplify their accounting workflows.

Key Features

• Payroll Management: Automates payroll processes, including tax calculations, employee benefits, and compliance.
• Inventory Tracking: Seamlessly manages stock levels, cost of goods sold, and product reporting.
• Tax Management: Helps e-commerce businesses comply with GST, VAT, and local taxes.
• Multi-Currency Support: Handles international sales and payments in multiple currencies, adjusting for real-time exchange rates.
• Cloud-Based Access: Allows access from anywhere, making remote teams and global operations convenient.

Pros:

• Ideal for small to medium-sized ecommerce businesses.
• Strong payroll management and tax compliance tools.
• Automates many accounting functions and integrates them with e-commerce platforms.
• Good inventory management and reporting capabilities.
  

9. Kashoo

Kashoo is a cloud-based accounting software for small ecommerce businesses seeking simplicity and efficiency. It automates key tasks like invoicing, expense tracking, and tax calculations, streamlining financial management for business owners. With an intuitive interface, Kashoo helps users stay organized and compliant without complex procedures. Its user-friendly features help with quick setup and easy financial management, making it an ideal solution for businesses looking to save time and reduce manual accounting efforts. Kashoo provides a simple, effective way to manage day-to-day financial tasks.

Key Features:

• Automated Invoicing: Set up recurring invoices and automate reminders to ensure timely payments.
• Expense Tracking: Automatically categorize expenses and track spending against budgets.
• Tax Support: Simplifies sales tax calculations and supports tax filing in various jurisdictions.
• Bank Syncing: Automatically syncs with bank accounts for seamless reconciliation of transactions.
• Mobile App: Offers mobile functionality for managing finances on the go.

Pros:

• Simple, affordable, and easy-to-use accounting software.
• Automated invoicing and tax calculations for seamless business operations.
• Good for businesses with straightforward accounting needs.
• Integrates with payment platforms like PayPal and Stripe.
  

10. A2X

A2X is an accounting software that seamlessly integrates e-commerce platforms like Shopify and Amazon with accounting systems. It automates transaction reconciliation and generates accurate financial reports, simplifying accounting for businesses with high-volume sales across multiple platforms. A2X eliminates manual data entry and ensures precise financial tracking, making it an ideal choice for ecommerce businesses that need to manage complex transactions. By streamlining accounting processes, this accounting software in ecommerce helps save time and reduce errors, allowing easier financial management and smoother reporting.

Key Features:

• Ecommerce Platform Integration: Directly integrates with platforms like Shopify, Amazon, and eBay for automatic transaction import.
• Automated Accounting Entries: Creates detailed, accurate accounting entries for every sale, refund, and fee automatically.
• Multi-Currency Handling: Supports transactions in multiple currencies, adjusting for exchange rates.
• Accurate Financial Reporting: Generates accurate financial reports for easier reconciliation and tax filing.
• Scalability: Designed to scale with growing businesses and handle high transaction volumes without manual effort.

Pros:

• Specifically designed for e-commerce businesses selling on platforms like Shopify and Amazon.
• Automates transaction reconciliation and financial report generation.
• Integrates seamlessly with accounting software like QuickBooks and Xero.
• Great for high-volume businesses with multiple sales channels.

Conclusion 

With the rapid changes in the ecommerce space, accounting software will play an increasingly vital role in managing the financial complexities of online businesses. The future of accounting software for e-commerce looks promising, with greater automation, improved scalability, and enhanced integrations to drive operational efficiency and growth. Therefore, to successfully navigate these advancements, businesses must partner with experts who can provide specialized insights and ensure that their accounting systems are implemented and optimized effectively.

At Invensis, we offer eCommerce Accounting & Bookkeeping Services to help e-commerce businesses streamline their financial operations using the latest accounting software solutions. From automating invoicing and tax calculations to integrating payment gateways and inventory management, we provide end-to-end support to enhance financial transparency and decision-making. Contact us to utilize our expertise in financial technology and ensure your e-commerce business stays ahead in the dynamic digital marketplace with our expert finance and accounting services.