10 Best Shopify Accounting Software Tools for Sellers


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As a Shopify seller, it’s important to have a good accounting system in place to track your income and expenses. There are a number of different accounting tools available, and choosing the right one can be tricky.


In this blog post, we’ll take a look at some of the best Shopify accounting tools to help you make the right decision for your business. 


What Features Do the Best Shopify Accounting Software Have?


The best accounting software for Shopify sellers will have a number of features that make it easy to track your sales and expenses, as well as manage your inventory.


Some of the features you should look for include: 


  • Easy-to-Use Interface: The software should be easy to navigate and use so that you can quickly find the information you need.
  • Sales Tracking: The software should allow you to easily track your sales so that you can see how much revenue you are generating.
  • Expense Tracking: The software should also allow you to track your expenses so that you can see where your money is going and identify any areas where you may be able to save money.
  • Inventory Management: If you sell products through your Shopify store, then the accounting software should also offer inventory management features so that you can keep track of your stock levels and reorder products when necessary.
  • Reports: The software should generate reports that you can use to track your progress and performance over time.
  • Customer Support: If you have any questions or problems with the software, then customer support should be available to help you resolve any issues. 


Quickbooks Online – for overall popularity


shopify accounting



QuickBooks Online is one of the most popular shopify accounting software options for small businesses. It has a user-friendly interface and offers a variety of features to help manage your finances.


Some of the features that QuickBooks Online offers include: 


  • The ability to track inventory and sales
  • A customizable chart of accounts
  • Automatic bank reconciliation
  • Invoice and bill tracking
  • Detailed reports and analytics
  • Integrations with other business software


While QuickBooks Online does have a monthly subscription fee, it also offers a free trial so you can try it out before committing to it.


Cons of Quickbooks 


  • The monthly subscription fee can be expensive for some small businesses
  • The interface can be confusing for some users
  • Some features are only available with the paid subscription 


Xero – for automation



When it comes to online accounting software, Xero is one of the best. Xero is a cloud-based software that offers a range of features for businesses of all sizes. One of the best features of Xero is its automation capabilities.


With Xero, you can automate a range of tasks, from invoicing and bill payments to bank reconciliation and financial reporting. This means that you can save time on administrative tasks, and focus on running your business.


Xero also offers a comprehensive range of features for managing your finances. You can track your income and expenses, create budgets, and run reports to get insights into your business finances. Plus, with Xero’s mobile app, you can manage your finances on the go.


If you’re looking for accounting software that offers automation capabilities and a comprehensive range of features, then Xero is the perfect option for you. 





If you’re looking for the best Shopify accounting software, Freshbooks is a great option. Here’s what you can expect from this powerful accounting tool: 


  • Ease of use: Freshbooks is designed to be simple and straightforward, so you can get your books in order without any headaches.
  • Invoicing and payments: With Freshbooks, you can easily create and send invoices, as well as accept payments online.
  • Expense tracking: Stay on top of your expenses with Freshbooks’ easy-to-use expense tracking features.
  • Reporting: Get detailed insights into your business with Freshbooks’ robust reporting tools.
  • Integrations: Freshbooks integrates with a variety of popular business tools, so you can manage all your finances in one place. 




shopify accounting


Wave is a leading accounting software that allows businesses to manage their finances and keep track of their spending. This software is best due to its compatibility so you can easily connect your Shopify store to your Wave account. This will allow you to manage your finances in one place and make it easier to keep track of your spending. 


Zoho Books



Zoho Books is a great option for Shopify accounting software. It has all the features you need to manage your finances, including invoicing, tracking expenses, and creating reports.


Plus, Zoho Books integrates seamlessly with Shopify, so you can manage your online store and accounting in one place. This makes it easy to keep track of your finances and make sure your books are always up-to-date.


If you’re looking for affordable, easy-to-use accounting software that will save you time and help you run your business more efficiently, then Zoho Books is  the perfect solution for you. 


A2X – for connections


shopify accounting


A2X is a great accounting software for Shopify businesses because it offers a number of features that can save time and improve accuracy.


One of the most important features of A2X is its ability to connect to Shopify. This connection allows businesses to automatically sync their sales data with their accounting software, which can save a lot of time and reduce the chance of errors.


Another great feature of A2X is its reporting capabilities. The software can generate detailed reports that can help businesses track their performance and make informed decisions about their finances.


Overall, A2X is a great option for businesses that are looking for accounting software that offers a number of features to save time and improve accuracy. 


ConnectBooks – for connections



ConnectBooks is an online accounting software that helps businesses keep track of their finances and make better decisions about their money. The software provides users with a real-time view of their financial situation, so they can see where their money is going and make better choices about how to spend it. ConnectBooks also offers a variety of features to help businesses manage their finances more effectively, including: 


  • A budgeting tool to help businesses track their spending and stay on budget
  • A invoicing system to help businesses keep track of their income and expenses
  • A payments system to help businesses accept and track payments from customers
  • A reporting system to help businesses understand their financial data


ConnectBooks is a great choice for businesses of all sizes that need a simple, effective way to manage their finances. 


LinkMyBooks – for connections


shopify accounting


LinkMyBooks is the best Shopify accounting software because it connects to your Shopify account and automatically syncs your sales data. This means that you can see your sales data in real-time, without having to manually input it into your accounting software.


LinkMyBooks also offers a variety of other features that make it the best Shopify accounting software, including:

  • real-time data sync
  • invoice and expense tracking
  • automatic bank reconciliation
  • financial reporting
  • tax compliance
  • and more!


EcomBalance – for a hands-off solution


shopify accounting


EcomBalance is the solution for those who want hands-off accounting software. With EcomBalance, all you need to do is connect your Shopify account and it will automatically sync with your accounting software.


There’s no need to manually enter data or reconcile accounts. Everything is taken care of for you, so you can focus on running your business.


EcomBalance is also very affordable, starting at just $249/month. It’s the perfect solution for small businesses that want an easy and affordable way to manage their finances. 


NetSuite – for larger companies



Larger companies have different accounting needs than small businesses and startups. They need an accounting solution that can handle their complex financials, inventory, and compliance requirements. That’s where NetSuite comes in.


NetSuite is a cloud-based accounting software solution designed specifically for larger businesses. It offers all the features you’d expect from a robust accounting solution, plus a few extras that make it ideal for larger companies.


Here are some of the key features that make NetSuite the best accounting software for larger businesses: 


  • Complex financial management: NetSuite can handle all your complex financial needs, from multi-currency to multi-company consolidations.
  • Inventory management: NetSuite’s inventory management features are second to none, making it easy to track and manage your stock levels across multiple locations.
  • Compliance: NetSuite helps you stay compliant with all the latest tax and regulatory requirements, ensuring you’re always up to date with the latest compliance standards.
  • Flexible deployment options: NetSuite offers both on-premise and cloud-based deployment options, so you can choose the option that best suits your business needs.
  • Scalability: NetSuite is scalable, so it can grow with your business as your needs change over time.


If you’re looking for an accounting solution that can handle all your complex financial needs, NetSuite is a perfect choice.



  • NetSuite is a complex solution that may be overkill for some businesses.
  • NetSuite can be expensive, so it may not be the best choice for businesses on a tight budget. 


Final Thoughts on Shopify Accounting Software


When it comes to accounting software for your Shopify store, there are a few key features to look for. First and foremost, you want something that will be easy to use and understand. The best accounting software will have a user-friendly interface that makes it simple to input your data and track your finances.


Another important feature to look for is robust reporting capabilities. The best accounting software will offer a variety of reports so that you can get a clear picture of your financial situation. This is especially important if you have multiple Shopify stores or if you run a complex business.


Finally, you want to make sure that the accounting software you choose integrates seamlessly with Shopify. The last thing you want is to have to export and import data between different platforms. Look for an accounting solution that offers seamless integration with Shopify so that you can keep all of your data in one place.

Want bookkeeping off your plate? We’ve got you! Get started, Speak w/ a Founder, or Schedule a Callback

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Kayla Bloom

Kayla Bloom is a freelance Finance Writer specializing in topics related to Accounting, Bookkeeping, Taxes, and Business Finances. She lives in Miami, Florida.

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