Accounting for Shopify: Start by Choosing the Right Software

accounting for shopify

Over the last two years, sales from online purchases almost doubled from 13.6 percent of all global sales to 19.5 percent. This percentage rate is expected to grow, and researchers predict that global online sales will soon reach a staggering 4.89 trillion dollars. This rise in online sales certainly has been helped by the ease of shopping online with platforms such as Shopify. Over 1,000,000 businesses are hosted by Shopify online stores in 175 different countries.

While Shopify has created a user-friendly online store software option that makes opening a whole business possible in one day, it does not address every need of a shop owner. Solutions for complete financial management and planning must be coupled with Shopify to achieve a healthy bottom line for your business. Luckily, there are a few options to choose from that answer this need of accounting for Shopify.

Apart from choosing accounting software that integrates with Shopify, you also want to work with an accountant – like our eCommerce accountants – that specializes in Shopify bookkeeping, taxes, accounting software setup, and more.

QuickBooks for eCommerce

QuickBooks is perhaps the most popular option to help manage the finances in your Shopify store, and Quickbooks Online makes it even simpler to handle your business wherever you are. QuickBooks Online allows you to break down expenses and categorize income easily automatically. The program has customized reports that will enable you to analyze sales and determine which items in your Shopify store are the most profitable.

QuickBooks Online seamlessly integrates with your Shopify store so transactions can be downloaded directly into the program. You can also create rules for the software to follow when downloading transactions which help the program to automatically categorize income and expenses, saving you a tremendous amount of time. 

Perhaps the most attractive aspect of QuickBooks online accounting for Shopify is that it is online. No matter where you are, you should always be able to stay informed and in control of your online store’s financial performance.

Read more about our QuickBooks bookkeeping services

Do You Need Assistance with Shopify Accounting or Software Integration?


One of the most significant challenges of Shopify online store owners is managing supply chain issues and keeping track of invoices. NetSuite is an excellent accounting for Shopify solution that answers these issues and many more. NetSuite integrates with Shopify in real-time through the Shopify app. NetSuite offers more overall management software by tracking inventory, product pricing, and sync customers with orders.

In addition, NetSuite provides methods to integrate with customers and provide informed customer service. You will also have additional opportunities to track orders and monitor fulfillment. Pair this with Shopify accountant services, and you have a complete financial and business management system.

Explore NetSuite SuiteCommerce that answers the need for ERP for online stores


Xero accounting for Shopify downloads all transactions automatically each day. You will have the opportunity to separate your vendors to compare performance side by side, and they offer excellent reports to help you analyze your business. If you choose to do business overseas, Xero helps to track appropriate taxes to be collected and monetary conversions.

Customer support is excellent with Xero, and you can always get help when you need it. Xero is a pretty standard solution used by Shopify accountants, and there is a nominal learning curve when setting up your integration and management with Xero.

Check out our Xero accounting, tax preparation, and more

Get in Touch

While there are many accounting options for Shopify, it is essential to be sure you have support solutions for every aspect of your business. At Fusion CPA, we have years of experience working with successful Shopify store owners. As Shopify accountants, We work hard every day to help our clients grow their businesses and find the financial security they are searching for online. We know that every business is different, and we will build a company platform that meets your needs. No matter what type of Shopify store you have, we’ll do all we can to offer an accounting solution that makes running your business as simple as possible.


This blog article is not intended to be the rendering of legal, accounting, tax advice or other professional services. Articles are based on current or proposed tax rules at the time they are written and older posts are not updated for tax rule changes. We expressly disclaim all liability in regard to actions taken or not taken based on the contents of this blog as well as the use or interpretation of this information. Information provided on this website is not all-inclusive and such information should not be relied upon as being all-inclusive.