Top 5 Accounting Software for Shopify Sellers

June 26, 2023

Looking for the best accounting software for your Shopify store? Find out which software is right for you in our comprehensive guide

 Looking for the best accounting software for your Shopify store? Find out which software is right for you in our comprehensive guide

You’ve set up your Shopify store, chosen the products you wish to sell, but now you need to have access to accurate financials in order to maximize your revenue. You can only do this by mastering your ecommerce accounting and ecommerce bookkeeping 

There are so many accounting software options out there for your Shopify store, including AI accounting and AI bookkeeping—but which one is the best one for you?

Is AI bookkeeping right for your business? Take this quiz to find out.

Well it really depends on your business size, budget, specific accounting needs, and the level of integration required with Shopify. Make sure to carry out your due diligence by exploring the features, pricing, and customer reviews of each software to make sure it fits your needs and can grow your business.

Lets dive in!

Here are our top 5 best accounting software for Shopify sellers

1) QuickBooks Online

QuickBooks Online dashboard

The OG of developed bookkeeping software, Intuit’s QuickBooks Online is one of the most recognized and widely used accounting software available in the U.S. and offers automation across your ecommerce store. 

While QuickBooks is a comprehensive cloud accounting software only and not an accounting service, if you don’t have accounting or bookkeeping knowledge, QuickBooks can be fairly time-consuming and complex. It can be a good fit for you if you have intermediate to advanced accounting knowledge—which is it's a preferred choice for many CPAs).

Shopify Integration

Quickbooks has a connector app that enables you to integrate your Shopify store and automatically imports sales and payouts, mapping them to the relevant accounts. You can also link your Shopify store directly from your QuickBooks account.

Key Features

  • Automatic matching: Automatically breaks down fees, taxes, and revenue across your sales channel and maps the payouts with the bank deposits.
  • Trend analysis: Provides valuable information about your sales, revenue, and best-selling items. Generates comprehensive reports that analyze your business performance across various sales channels.
  • Tax management: With its automated financial breakdowns, QuickBooks simplifies tax time by maximizing your deductions, ensuring a smoother tax filing experience.


Prices start from $15 for the Simple Start edition but you would likely need to upgrade to a higher tier starting at $27.50 per month to get the functionality you need to manage your books. You will have to add necessary app integrations, such as A2X which starts at $19 a month.


2) Xero

Xero's cloud-based accounting dashboard

Another favorite amongst many accountants and bookkeepers, Xero is a cloud-based accounting software for small and medium-sized businesses. It offers a range of features similar to QuickBooks Online, such as double-entry accounting, reporting, bank reconciliation, an inventory module, and various integration options.

You can also customize your dashboard to review all your ecommerce metrics at once.

However, just like QuickBooks, Xero functions solely as accounting software and still requires you or your bookkeeper/accountant to handle the DIY accounting tasks.

Shopify Integration

You can download the Xero and Shopify integration from the Xero App Store. Xero seamlessly integrates with Shopify, allowing your sales data to flow automatically into the Xero accounting software. Xero also has over 800 integrations with other third-party applications.

Key Features

  • Unlimited users:  Freedom to add as many users as you want and give each user different levels of control and access.
  • Invoicing and quotes: Offers invoice customization together with a convenient feature for creating and sending quotes, recurring invoices, and automatic reminders. 
  • Expense tracking: Effortlessly links your credit card and bank account directly so you can categorize expenses, split transactions, and remember previous transactions.


Prices start from $12 per month, but for the extra features, you may want to upgrade to the $34 per month plan. Just like with QuickBooks you will have to add app integrations like A2X, starting at $19 a month. 

3) Zoho Books

Zoho Books customized sales and purchase transaction template

Zoho Books is a comprehensive platform for managing your bookkeeping tasks and organizing your transactions—handles your company’s bills and invoices, reconciles bank statements, and controls spending in a single, secure location.

Shopify Integration

Zoho Books allows you to sync your Shopify sales data, providing you with a clear overview of your business finances. 

Key Features

  • Customization: Tailor sales and purchase transaction templates to suit business needs and reflect your brand identity. Adapt sales and purchase transaction templates to meet the requirements of your business.
  • Automation: Streamlines task prioritization and handles multiple tasks through automated workflows, including email notifications, field modifications, and in-app messages.
  • Document management: Documents can also be emailed directly to your inbox where they are automatically categorized and processed. Establishes a centralized hub for all your documents, allowing you to upload and attach files such as receipts and transaction records. 


Zoho is free for businesses who have less than $50,000 per year in revenue; paid plans start at $15 per month.

4) FreshBooks

FreshBooks dashboard accessible on mobile and desktop

FreshBooks is an accounting software with a reputation for being easy to set up and use and for having excellent customer service. FreshBooks is cheaper than QuickBooks but is more limited in its features. 

FreshBooks offers an intuitive dashboard, and basic features for tracking income and expenses at an affordable cost-income, while automatically reconciling credit and debit amounts.  However, it may not be the ideal choice for larger businesses and additional charges apply for multiple users, and similar to QuickBooks and Xero, it would require you to invest the time to learn the system and maintain your books yourself. 

Shopify Integration

FreshBooks gives you access to built-in Shopify accounting integration so that you can make full use of the best accounting software for Shopify drop shippers.

Key ‍Features

  • Customizable Invoicing: Provides a robust invoicing system that allows you to create professional-looking invoices and customize them to match your brand. You can easily track sent invoices, set up automatic payment reminders, and accept online payments.
  • Expense Tracking: Easily track your business expenses by capturing receipts, categorizing expenses, and attaching them to specific projects or clients. 
  • Mobile Apps:  Through FreshBooks’ mobile apps for iOS and Android devices you can create and send invoices, track expenses, and view financial reports directly from your mobile device which automatically syncs to your desktop.


Plans start at $8.50 per month for the basic plan plus the cost of the third-party app integrations.


5) Finaloop

Finaloop's fully reconciled ecommerce-tailored P&L breakdown for Shopify

Finaloop is the only automated, e-commerce tailored full bookkeeping service for ecommerce businesses selling on online store platforms like Shopify or Woocommerce or marketplaces like Amazon, Walmart, eBay, etc. Finaloop is different from QuickBooks and Xero in that it includes not only an accounting software but also an accounting service as well as its own in-house app integrations.

Finaloop’s uses AI technology and ecommerce-focused expertise to fully reconcile financial data in real-time, providing ecommerce and DTC brands flawless books, optimized tax returns, and actionable insights 24/7. Finaloop also has real-time sales channel integrations, accrual/cash basis flexibility, real-time P&L and balance sheet, and AI-driven expense categorization, together with expert review and support from a dedicated and responsive bookkeeping team.

Shopify Integration

Finaloop’s integration connects to your Shopify account as well as other relevant apps to integrate all of your data into your books.

Key Features

  • Real-time automated COGS (Cost of Goods Sold) tracker: Automatically syncs COGS to the P&L in real-time for Shopify orders and includes an SKU-by-SKU (Stock Keeping Unit) breakdown, allowing full financial visibility without waiting until the month is over. 
  • Connects to sales channels and payment processors: Finaloop connects to your sales channels and payment gateways, pulls in your data in real-time, and automatically maps them to your P&L and balance sheet based on tax rules and best accounting practices. 
  • Real-time, 100% accurate, cash-flow analysis report: The report allows DTC and ecommerce brands to analyze your cash-flow at any time from anywhere.


Prices start from $65 per month (depending on your expected annual sales). It costs more than the basic plans of QuickBooks and Xero since it includes accounting services as well as the app integrations.


A major consideration you need to have when choosing the right accounting software for your Shopify store, is whether you want a DIY accounting software only that you would spend the time managing yourself or do you also want a service that saves you time on the actual bookkeeping tasks. 

QuickBooks Online, Xero, Zoho Books and FreshBooks—while all great options—require you to pay extra for a bookkeeper or accountant in order to give you the full picture of your financials.

If you are looking to spend less time on bookkeeping each month by outsourcing it, Finaloop is a great choice since it's significantly cheaper than traditional bookkeepers or accountants, is tailored specifically to e-commerce, thereby providing you with more accurate and real-time ecommerce-based financials. 

Sign up HERE to get your financials set up today.

About Finaloop

We are a technology company providing automated end-to-end accounting service to ecommerce businesses. Our system connects to your apps, syncs all your data and reconciles your books in real-time, replacing your bookkeeper, your accounting software, and your ecomm integrations. We offer reconciled books available 24/7, tax-saving insights, and a single place for all your financial data.

*The information provided on this website does not, and is not intended to, constitute legal advice. All information, content, and materials available on this site are for general informational purposes only. Readers are advised to consult with their attorney or accountant with any questions or concerns.*

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