Four Best Accounting Software for E-Commerce Businesses

Posted by Jan Victor Valencia
Apr 06, 2022
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Choosing the accounting software for your E-Commerce business is a different challenge by itself. There are tons of great options out there, but you need to find one that suits your business needs.

Lucky for you, we have narrowed down your list and selected the four best accounting software for E-Commerce businesses.



1. QuickBooks Online

Starts at US$ 25.00/mo.

Best Feature: Direct integration with E-Commerce platforms 

Cons: Steeper learning curve for advanced features 


QuickBooks Online (QBO) is one of the leading cloud accounting software in the industry. QBO made great leaps in providing easy-to-use accounting solutions to E-Commerce businesses through seamless platform and apps integration. While advanced features have a steep learning curve, the essentials are intuitive and helpful to business owners. 


2. Xero

Starts at US$ 12.00/mo. 

Best Feature: Over 700 add-ons 

Cons: No direct integration with Shopify

Xero is a cloud accounting software with small business owners in mind. The software is affordable, easy-to-use and allows you to create multiple users in any of its plans. With over 700 add-ons available, Xero is one of the most versatile software in this list. While the lack of direct integration with Shopify will raise brows, these add-ons can surely help you sync your records. 


3. Wave


Best Feature: Free software 

Cons: Limited accounting features

Wave is a good option for E-Commerce businesses that are looking for an accounting software at the lowest possible cost. This free accounting software covers the basic needs of an E-Commerce business. However, those aggressively expanding may soon need more tools to cater to their needs. 


4. FreshBooks

Starts at US$ 6.00/mo.

Best Feature: Direct integrations with Shopify and Squarespace 

Cons: Plan limits on billable clients

FreshBooks is another cloud accounting software created with small businesses in mind. It has direct integration with Shopify and Squarespace making it attractive for E-Commerce businesses that are just getting started. Their affordable pricing plans for FreshBooks are setup based on the number of clients that a user can bill. 


We hope these cloud accounting software can help your E-Commerce business get to a good start. These software offer great features but always choose the one that fits your needs.


Can’t decide which cloud accounting software is best for your E-Commerce business? Contact us at for a free consultation with one of our accounting experts. You may also download our Succeeding Online: Refining Your Accounting Processes through Technology and Automation to know more about our E-Commerce accounting solutions.


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