Best Accounting Software for Shopify (Our 2022 Top Picks)

Shopify is one of the most popular eCommerce platforms in the world. It is the third-largest online store in the United States after Amazon and eBay, commanding a 23% market share. If you are one of the 1.7 million merchants who use Shopify, you might be wondering which Shopify accounting software will work best for your business.

Many Shopify accounting software options are available, and choosing the best can be overwhelming. In this article, we will discuss the best accounting software for Shopify. We will look at the features and pricing of each software as well as the pros and cons so that you can make an informed decision.

Things to Look for in the Shopify Accounting Software

Before we discuss the best Shopify accounting software, let's take a look at the features you should consider when making your decision.

Ease of Use

The last thing you want is accounting software that is difficult to use. The best Shopify accounting software should be easy to navigate and understand. It should have an intuitive interface that even a beginner can use.

Customer Support

The accounting software should have excellent customer support so that you can get help when you need it. The type of customer support options available varies from one software to another. Some offer 24/7 live chat and phone calls, while others only have email contact options or community forums.


The accounting software you choose should have strong encryption to keep your data safe from hackers. It should also be compliant with industry standards such as the Payment Card Industry Data Security Standard (PCI DSS). With compliance, you can ensure that your customers' payment information will not get into the wrong hands.

Best Shopify Accounting Software for 2022

Here is the best Shopify accounting software for 2022:


Xero is an easy-to-use cloud accounting software that syncs seamlessly with your Shopify store. It has many useful features including real-time reporting, purchase tracking, automatic bank feeds, and multi-currency support.

In addition to being a comprehensive accounting software solution, Xero also offers numerous apps. These can help with everything from online invoicing to payroll management.

What makes Xero stand out is its multi-user functionality. This function allows you to add as many users as you want. You can also limit their access rights so that users only have the information and features they need for their particular role in your business.


  • Easy to use. Xero is one of the easiest accounting software to use. The interface is intuitive, and even a beginner can navigate it in no time.
  • Excellent customer support. Xero has excellent customer support with 24/7 live chat, phone call, and email options.
  • Integrates well with other apps. Xero integrates seamlessly with Shopify and many other apps. This allows you to streamline your workflow and save time.
  • Scalable. Xero is a scalable software that can grow your business.


  • Doesn't support Exchange Trade Products (ETPs). This can be a problem if you trade ETPs as Xero does not support them.


We cannot talk about the best accounting software for Shopify and not mention QuickBooks. It is one of the most popular accounting software available and is used by millions of businesses worldwide.

QuickBooks is a comprehensive software that offers everything from invoicing to bookkeeping to payroll management. In addition, it integrates well with other apps so you can manage your entire business from a single platform.


  • Comprehensive. QuickBooks is comprehensive accounting software that offers everything you need to run your business efficiently.
  • Easy to find and fix errors. QuickBooks has an excellent error-finding and -fixing feature. This makes it easy to troubleshoot any problems that may arise.
  • Easy integration. This accounting software can be easily integrated with other apps to streamline your workflow.


  • Lack of direct professional support. This software doesn't offer direct professional support. You can only seek assistance from the community forum or Twitter account.
  • File size limitations. File size limitations may create problems when you have large files to upload.

Zoho Books

Zoho is one of the leading names in cloud-based accounting software. It has become a popular choice among Shopify merchants who want to integrate their store with an easy-to-use system.

With this accounting software, you can manage your invoices, expenses, inventory items, and general business activities from a single dashboard. It also offers additional features such as multi-currency support.

Some of the most notable features of this Shopify accounting software include its easy-to-use interface and its ability to track time spent on projects and generate invoices for them automatically.


  • Easy integration. Integrating this Shopify accounting software with other tools is very simple.
  • Easy to use. Zoho Books features an easy-to-use interface that anyone with basic accounting and computer skills can use.
  • Affordable. This software offers a free plan which you can test out before paying real money. Paid plans are also very affordable compared to other similar accounting software options of its caliber.


  • Limited features in the free plan. The free version of this software comes with limited features, which may not be sufficient for most people.
  • Limited integration options. Even though this software integrates with many apps, it is still not as many as some of the other leading accounting software options.


One of the best accounting software for Shopify that cannot be overlooked is Sage. It offers everything from invoicing and expense tracking to asset depreciation and job costing.

What makes this software a great option for businesses of all sizes is its ability to scale with your business. As your business grows, Sage will grow with you without any limitations.

This Shopify accounting software is highly customizable. As such, it is a great option for businesses that need to customize their tools to meet their specific needs.


  • Comprehensive. Sage is one of the most comprehensive Shopify accounting software options today. It offers everything you need to manage your books and finances.
  • Customizable. This software is highly customizable. You can customize it to meet your specific needs without any limitations or restrictions.
  • Strong inventory reporting capabilities. Sage has strong inventory reporting capabilities that allow you to stay on top of your stock.
  • Industry-specific features. With this accounting software for Shopify, you can get industry-specific features such as product tracking and job costing.


  • Complex for novices. Sage can be complex for novices. It is not a good option for businesses looking for accounting software that is easy to use.
  • Not effective for a journal entry. Sage is not the best option for journal entries. It can be challenging to make adjustments in your books using this accounting software for Shopify.


Another great accounting software for Shopify is Botkeeper. With this platform, you can easily automate your bookkeeping and accounting tasks.

All of your transactions get recorded automatically in real-time. Therefore, you don't have to worry about missing anything or losing track of anything important. It also automates reconciliation which means less work for you and more time to grow your business.

Botkeeper has many useful features. They include automatic transaction categorization, unlimited support, data security with bank-level encryption standards (SSL), and more.


  • Accurate reporting. Botkeeper offers accurate reporting that you can rely on to make important business decisions.
  • Customizable reports. With this software, you can customize your reports to fit your specific needs and requirements.
  • Efficient customer support. Botkeeper has good customer support that consists of experienced professionals willing to help with any issues or concerns related to their product or service offering(s).


  • No free trial. Botkeeper doesn't have a free trial. You have to pay for their service to use it.
  • No detailed resources. Botkeeper’s website doesn't have a lot of detailed resources. This can be frustrating for first-time users trying to learn more about the product and its features.


If you are looking for a Shopify accounting software that is simple to use and affordable, Bench may be a good option for you.

This software is perfect for small businesses that are just starting. It's also great for businesses that don't have the time or resources to manage their own accounting and bookkeeping tasks.

This human-assisted AI software gets financial data from connected credit cards and bank accounts to produce accurate reports and insights into your business.

Bench has many great features, including automated bookkeeping with the option of human assistance if needed, real-time financial reporting on income statements, balance sheets, and cash flow projections.


  • Fast and intuitive. It gets all of your financial data in one place so that you can make better business decisions more efficiently.
  • Suited for small businesses. If you have a growing business, Bench can help you manage your finances without hiring a full-time accountant.
  • Affordable. This software is affordable, and it's a great option for businesses that are on a tight budget.


  • Limited integrations. The only limitations with Bench are that they don't have a lot of integrations. This could make it difficult for businesses that want more control over their finances and integrate other software programs into the platform.
  • Less comprehensive. Unfortunately, this Shopify accounting software is not as comprehensive as others on the market. If you are looking for something with more features and functionality, this may not be your best option.


Choosing the right program for your business can be difficult. It's important to consider your specific needs and requirements before making a decision. Do you need a program that is fast and easy to use? Or do you need something more comprehensive with a lot of integrations?

Before you decide on the right one, it’s worth seeing if the software offers a free trial or a demo. This way, you can test it out first before you commit and see if it would suit your Shopify business needs. 

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