SMALL BUSINESS GROWTH   |   6 minute read

Which accounting software is right for your eCommerce business?

When it comes to choosing the best accounting software for eCommerce in 2017, small and medium businesses (SMBs) have many options. Not making the right choice can be both costly and time-consuming.

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Comparing the best

We reviewed the industry’s best accounting software for eCommerce businesses based on the following:

  • Functionality
  • Integrations
  • Price point
  • Customer support


The Xero accounting software program provides a wide range of eCommerce accounting procedures making it an ideal choice for a diverse range of small and medium sized online businesses.

The program easily deals with all aspects of eCommerce bookkeeping, from generating invoices and quotes to reconciling your bank balance. Xero has all the functions that you would expect from an industry standard eCommerce accounting software package, such as:

The system comes with full customer support and the various pricing options (starting at $6.30 a month after a 30% discount) making Xero value for money in terms of initial cost and ROI.

Find out more about Xero with this comprehensive review

QuickBooks Online

While QuickBooks may have been around for some time now, they are always working on improving their range of eCommerce bookkeeping and accounting software. QuickBooks Online provides a reliable and cost-effective Quickbooks eCommerce integration. It also has the benefit of being based on the robust framework of their globally successful tried and tested PC based bookkeeping system.

Features of the QuickBooks system include:

  • Easy-to-use navigation
  • Common accounting tasks at the push of a button
  • A range of advanced tools
  • Full sales recording with credit and debit card friendly invoices and payment notifications
  • Downloadable bank transactions
  • Categorises and reviews deposits and expenses
  • Full mobile integration

The system has a comprehensive online support facility and pricing is based on three scalable ongoing subscription levels (starting at $10 a month) that will scale with your business.

If you are looking for a cloud software program with the benefits of a proven track record in web based accounting and the ability to integrate with shopping cart platforms like Shopify, inventory and order management software like TradeGecko, along with other aspects of your eCommerce business, QuickBooks Online will tick all the boxes.



Sage has been around for over thirty years and has established a solid track record for supplying user-friendly accounting software packages. They’ve consolidated their knowledge gained from developing platforms and have now created an industry standard, cloud-based system that is both cost-effective and flexible.

What you get with Sage:

  • Fully integrated accounting and finance management
  • Payroll services
  • Access all your data in one place
  • Banking integration (automatic bank feeds import bank statements into your Sage account)
  • Full mobile integration for all users
  • Cloud-based software giving instant access to real-time data
  • Sharing and integration with apps like WooCommerce and Shopify
  • Full support and ongoing training (including Sage University)

Sage have established themselves as long-term experts in user-friendly business accounting. Their accounting software makes it easy to manage income and expenses, unlimited bank transactions, and even generate reports for better decision making. With pricing plans for every business type, from a small start-up to a rapidly growing international business, you’ll definitely be able to find the right plan for your business.


FreeAgent is the small and micro business accounting program that has many of the features that you would only expect from bigger accounting systems like Xero and Quickbooks. The easy-to-navigate dashboard provides users with drag and drop dashboard customization and up-to-the-minute accounting data. From time tracking and financial report generation to project overviews and full bank account integration, FreeAgent has everything a small business or freelancer requires.

FreeAgent features include:

  • Cloud-based system
  • Mobile app for iPhone and Android
  • Estimates and invoices
  • Photo receipt facility
  • Time tracking (record your time spent using the built-in stopwatch or smart timesheets)
  • Bank account connectability
  • Real-time project and performance monitoring
  • Support system that includes online guides, webinars, and email and telephone support

FreeAgent comes at the one affordable and fixed price of $20.00 a month and that includes a support system featuring start-up training, online help, knowledge base, and webinars. The system’s ease-of-use, photo invoicing facility, and app configuration make it especially attractive to small businesses and freelancers who are used to doing their accounting on the go.

While FreeAgent is a great tool for small businesses and freelancers, it’s less suitable for wholesalers and distributors who deal in large quantities of physical goods as it doesn’t let you create purchase orders or automatically track your inventory movement. Also, it’s hard to trace errors through FreeAgent as it does not come with an audit trail as a means to track what changes have been made.


Wave Accounting

For businesses that are just starting out or operating with a limited budget, Wave Accounting is the ideal double entry bookkeeping solution. From a full suite of standard accounting tools, credit card processing, and free mobile applications, this free online accounting software is an impressive system for a new business.

The features of Wave Accounting include:

  • Full double entry accounting functionality
  • Bank data importing
  • Invoicing and expense tracking
  • Customizable accounts charts
  • Offers integration with Shoeboxed and Etsy
  • Credit card processing and receipt scanning
  • Free mobile online functions

When it comes to value for money, Wave Accounting provides an easy option. Support is available through an online ticket system rather than a live helpdesk, so prospective users need to balance the risks of possible business downtime against the benefits of a free system.

Making the best accounting software for eCommerce choices for your business

We appreciate that no two businesses are the same and where your business is right now is not where it is going to be in a year’s time.  Scalability and flexibility should be two of the most important considerations unless you want to be faced with the prospect of outgrowing your software and funding the cost of replacement when your business expands.

Choosing the right accounting software for your business will save you time and money while allowing you to sell more products. Start a free trial with TradeGecko and find out how you can integrate your accounting software with our inventory management system today.

See also:
Free Inventory Spreadsheet: How to manage inventory in Excel
Stock Keeping Unit (SKU) Meaning - Why is SKU Important?

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