When you find the right accounting software, you can continue to enjoy all the flexibility that ecommerce provides while knowing that your accounting is under control. Of course, not all accounting solutions are created equal. It’s important that you find the best one for your business.

That’s why we’ve put together a list of the best accounting software options for ecommerce businesses. See which one you like the best.


QuickBooks Online

QuickBooks is consistently improving the range of bookkeeping and accounting software they offer for ecommerce businesses. The QuickBooks Online version is scalable, so it’s perfect for any small to medium-sized businesses. It’s also worth mentioning that QuickBooks has been around for a while, so it’s proven to be a tried and tested system that works.

Some of the best features you’ll find in QuickBooks Online are:

  • User-friendly navigation
  • Various accounting tasks available with one click
  • A wide range of more advanced accounting tools
  • Downloadable bank transactions
  • The ability to categorize and review expenses and deposits
  • Full sales recording with invoicing and payment notification options
  • Fully integrates with mobile use
  • Comprehensive online support

Pricing for QuickBooks Online is tiered, starting at just $10/month.



Xero accounting software is also a good choice for small and medium-sized online businesses. It includes features that cover all the components of ecommerce accounting including invoicing, bank statement reconciliation, and full customer support. Additionally, you will enjoy the following extras with a Xero integration:

  • Tax bundling
  • Payroll processing software
  • Multi-currency pricing
  • Cloud-based
  • Open API for easy integration with other ecommerce software
  • Banking functions

Pricing for Xero is tiered, starting at $9/month.



FreeAgent is a small accounting program with many of the bells and whistles any ecommerce business may need. It’s a perfect option for small businesses and freelancers, but may not be ideal for distributers and wholesalers who work with large quantities of products (it doesn’t include purchase order tracking or ecommerce inventory management).

The dashboard is easy to navigate, customizable, and consistently up-to-date. Some of the features the FreeAgent accounting software comes with are:

  • Bank account integration
  • Mobile-friendly
  • Cloud-based
  • Time tracking
  • Invoicing and estimates
  • Real-time monitoring for projects and performance
  • Comprehensive online support including start-up training and webinars

Pricing for FreeAgent is a flat $24/month, but U.S. users receive the first 6 months for only $12/month.



The name “Sage” is appropriate for this accounting software because it has been around for more than three decades with a proven track record of providing users with user-friendly software programs. Sage created a true industry standard with cloud-based solutions that are effective and flexible. Every size ecommerce business from start-up to fast-growing international companies will benefit from this software.

Features that you’ll enjoy with Sage include:

  • Payroll options
  • Full banking integration
  • Mobile integration
  • Cloud-based
  • Fully integrated financial management and accounting
  • Comprehensive online support and education with Sage University

Pricing for Sage accounting software starts at $10/month and is tiered for larger businesses.


Wave Accounting

Wave Accounting is an option for businesses that are just starting or have limited budgets. It offers a full suite of accounting tools, card processing, and free mobile apps. However, they don’t provide any inventory tracking features or customization options. Additionally, Wave provides:

  • Double entry accounting functions
  • Importing bank information
  • Expense tracking
  • Invoicing

Pricing for Wave Accounting is tiered based on additional features. The basic accounting plan is free.


Make the Best Choice of Accounting Software for Your Ecommerce Business

No two ecommerce businesses are the same and what may work for your business now, doesn’t mean it will work next year. Finding the right accounting system, one that is effective for your business now and flexible and scalable for the future, will save you time and money, helping your business continue to grow.

Need more help with ecommerce accounting? Check out this post for a deep dive in chart of accounts and more.

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