Best Accounting Software for Shopify in 2021

We ranked Freshbooks as the best Best Accounting Software for Shopify in 2021 in our roundup. Click here to get 50% off for 3 Months Get 30-Days free trial


Freshbooks is a small business accounting and bookkeeping software that makes running your business a breeze.

Deployed on: Cloud

Starting From: $4.5 / month


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Sage is an entry level accounting and bookkeeping software that is ideal for SMBs and businesses want to manage their cash flow.

Deployed on: Cloud

Starting From: $10 /month


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Quickbooks by Intuit

The complete accounting toolset whether you're a freelancer or a Forbes 100 company.

Deployed on: Cloud

Starting From: $4.5 /month


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NetSuite by Oracle

One of the best cloud-based financial management solutions for medium to large organizations. It integrates with all other NetSuite order management, inventory, CRM and eCommerce functions to streamline critical business processes.

Deployed on: Cloud

Starting From: $999


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Xero is a cloud-based accounting software for medium to big enterprises

Deployed on: Cloud

Starting From: $9 / month


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Buyer's Guide

Using the right accounting software for your Shopify store you can always stay on top of your finances and make sure your online store is in good standing, both in financial and tax-wise. These helping software also makes sure that your Shopify online store covers all the legal requirements your local tax authority enforces. 

Picking the best accounting software for your shopify online store is important. Whether you're just getting started selling online or have an already established dropshipping or an e-commerce business, accounting is a vital part of your establishment. The solutions we reviewed in our buying guide will help you pick the right one for you.

What should you look for in a Shopify accounting software?

Like in many other products you use, there's not a one solution fits all accounting software. First you need to establish what features your business ultimately requires. The industry your company operates in, its size and the product type plays a vital role in determining the right program. Once you have a rough answer to these questions, you may look at the options we have provided in our comparison table. 

In a nutshell, regardless of the solution you pick, it must be tailored to your type of business. As long as you don't have to prepare balance sheets, a revenue surplus calculation, manually record your documents and write invoices, it is sufficient for the profit and loss calculation of your company. 

After making sure your pick covers your basic needs, other features you can look for include but not limited to; 

  • Easy to use & understand user interface with an extensive usage guide.
  • It's legally compliant with your local tax authority.
  • Automatically syncs data between your other accounts
  • Preferably cloud based so you can access your data and finances wherever you are, whenever you need.
  • Cross-platform: It should be able to work on Windows as well as MAC and mobile devices.
  • Quick overview of your Shopify store's financial overview.
  • Bookkeeping in compliance with your legal tax authority

For your company the software also must have essential control functions. It should enable you to keep track of all income and expenses and also analyse statistical evaluations. For example, online merchants should be able to easily tell if your company made profit in any month/quarter or it's bleeding money.


After covering the essentials above, the extra features we've listed below will definitely make your life easier, especially if you don't have a department dedicated to your e-commerce business' financials:


  • It should allow you to Import and export your Shopify store's accounting details
  • Data backup must be available to ensure you don't suffer unwanted data loss.
  • Automatic control recording (ELSTER interface)


Deployed on the cloud

It's almost 2021. most of dinasour desktop based accounting software most likely won't offer the solutions your Shopify store demands. So make sure your best pick is deployed on the cloud. It simply allows you to record, manage and access your data on the go as long as you have internet access.

Cloud solutions are usually suitable for online merchants if the provider also integrates banking and PayPal interfaces. Since well-functioning online stores can incur high billing costs since you'll be paying for hosting, domain, and many other Shopify apps, an accounting system on the cloud makes sense if all accounts and accounting transactions are visible at a glance.

An accounting software deployed the cloud can certainly be worthwhile for smaller online stores as well, especially since it's the most cost effective solution. 

Another advantage of cloud solutions is that external service providers such as accountants or tax consultants can access the program. This can greatly reduce the time and money you spend on your store's accounting and bookkeeping.

Cem Akbulut
Co-founder, 9to5Media.

Cem Akbulut is Co-founder & CEO of 9to5Media, a software research lab that provides advice, information, and tools to help businesses thrive.

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