Top Shopify Accounting Software for Your Ecommerce Business

Michael Pignatelli
Nov 25, 2022

Accounting software options abound in the ecommerce accounting world. However, most of the time, it's hard for online sellers to choose which one works best for them.

Because your business can grow rapidly in a short amount of time, choosing Shopify accounting software is a priority. Let Unloop narrow down your options so you can set up your accounting system before your Shopify store rakes in revenue.

QuickBooks Online

QuickBooks Online is one of, if not the most, popular accounting software. Most accountants and Shopify online store owners opt for this accounting tool. It has all the essential features needed by any ecommerce business owner—it can stand as a full accounting system on its own.

Feature Highlights

User-friendly Dashboard: QuickBooks has an easy-to-use dashboard that any business owner and accountant can glance at. From the dashboard, you’ll see a graphical and numerical representation of your Shopify sales, accounts payable, month-to-month cash flow, and other information. You can easily digest all this vital information in minutes.

Tax Support: What's awesome about QuickBooks is it works with sales tax from marketplaces such as Amazon. It can also select the income tax form applicable to your business structure. From there, the accounting software can map the transactions based on the line items of your business tax form, making it easy for you and your accountant to process taxation.

App Integration: You can integrate QuickBooks into ecommerce platforms. When this is done, sales and inventory will be synced with income records. Additionally, other accounting app integrations to QuickBooks can make payments of accounts payable obligations a breeze.

The Pros

If there's a noteworthy feature that QuickBooks Online has, it's the user-friendliness of the accounting software. No wonder it's the preferred accounting tool for professionals. It has advanced features that can compete with other comprehensive accounting software, but it is presented in a way that even non-accountants can understand.

The Cons

What makes QuickBooks a popular Shopify accounting software is also its drawback. QuickBooks is great for ecommerce businesses because of its inventory management features and real-time reporting of financial data. Still, it lacks industry-specific key metrics, which may impair financial and business management.

Xero Accounting Software

With over 1 million users, Xero has built a reputation as the accounting solution for the growing small business entrepreneur. Its web-based accounting solution is perfect for Shopify sellers who specialize in selling a few products, but with a huge market share and are ripe for scale.

Feature Highlights

Payroll Management: Xero's accounting software is built to bring small businesses and employees convenience in their ecommerce store. The software can integrate with a third-party app that makes payroll and tax calculation easy.

Security: Xero has a strict authentication feature that uses a security application from your mobile device. Apart from login security, Xero has a feature that integrates proper checks and balances within the software to ensure that no fraudulent activity is committed.

Reporting: With Xero's accounting software, ecommerce business owners and managers can better analyze financial data and make decisions. The reports you can generate within the accounting tool span a wide range, leaving you wanting nothing.

The Pros

Security and anti-fraud features make Xero an attractive option for Shopify store owners. It allows you to safeguard crucial information from unauthorized users while ensuring your accounting numbers aren't distorted. These two things are critical when your store is on top of the competition.

The Cons

Inventory management is functional. It has all the features you would expect from a typical accounting platform. But if you have a business with plenty of product and merchandise lines, it may be harder to track them with Xero's basic inventory management.


This accounting software has a lot of efficient features that make it attractive. Besides its agile expense tracking system, it also has a robust payable tracking feature that helps you manage your cash flow well. In addition, it's a tool for sellers heavy on business-to-business transactions and bulk purchasing.

Feature Highlights

Project Tracking: Freshbooks will bring the utmost benefit to Shopify business owners that outsource contractors. The accounting software uses time sheets and provides accurate and detailed information that contractors and business owners can use for disputes.

Expense Management: The Freshbooks accounting software has a robust expense tracking and recording system. You can download a mobile app, take pictures of receipts, and associate them with a particular expense record. This makes identifying and managing expenses significantly more convenient.

Financial Data Reporting: Freshbooks’s accounting system can generate financial reports such as a profit and loss statement or a balance sheet in just a few clicks. This way, you can see the health of your business given your business transaction records on the accounting software.

The Pros

Freshbooks is an accounting software that's excellent for entrepreneurs and accountants on-the-go. The combination of the mobile app and the expense tracking feature makes recording expenses seamless and collaborative. It is also perfect for Shopify sellers who produce their products, as they will be at the heart of their business's expenses.

The Cons

While Freshbooks is a competitive accounting software that can go toe-to-toe with other popular systems, it still has a few rough edges to refine. While minor, several bugs in the accounting software can inconvenience a user.

Sage 50cloud Accounting Software

Sage business cloud accounting software, formerly known as Peachtree. It is one of the best Shopify accounting software around. It's a comprehensive system that includes just about everything a business needs. In addition, it has an abundance of awesome features that improve Shopify businesses, including tax-ready financial reports, customized financial reporting, and more.

Feature Highlights

Information Customization: Sage 50 allows users to configure how they view the data they receive from different business transactions. This makes analyzing data easier for making better managerial and business decisions.

Invoice Management: Sage 50 allows an accountant or a Shopify business owner to issue and send invoices to clients. The invoice is sent to the client's email address with a pay button to make it easy to collect due accounts receivable. With this feature, it's easier to maintain a positive cash flow.

Customer Service: Sage 50 has a great customer support system built for ecommerce store owners and their accounting staff. Easily access Sage 50's knowledge base, watch a video tutorial, and talk to a representative via phone if you encounter issues with the software.

The Pros

Sage accounting software allows unlimited users on their cloud-based accounting software. For a fee, the owner or administrator can include additional accounting and business staff to access and manage the software. This makes collaboration easier for all the business stakeholders.

The Cons

If there's anything to be improved in the Sage 50 software, it's its user interface. The developers can design the dashboard section and its menu to be simpler. This can be a small improvement that will appeal to accountants using the software and online sellers wanting to manage their own financial data.

QuickBooks Is the Best Accounting Software

QuickBooks Online provides the best accounting solutions for ecommerce small business owners. It's got basic accounting that business owners can intuitively use—just learn the default chart of account categories and enter the numbers, and it will be good to go.

Apart from the simple interface and functionalities, it is a popular accounting software rich with integration features. Most third-party apps allow integration with QuickBooks, and many accounting service agencies specialize in the software. Thus, it’s convenient for a seller to get enough support if they want to scale up their accounting system and their business.

Get the Most of QuickBooks Online When Doing Accounting for Shopify

QuickBooks is the preferred accounting software for Shopify. But as a business owner with a lot of stuff to do, acquiring enough software and accounting knowledge can be a drag. So, get the most out of your QuickBooks subscription by getting accounting professionals to handle it for you. Here's what experts can bring to the table.


Accounting professionals who are also specialists know how to sync bank account transactions to QuickBooks and audit them. As a result, they can provide you with accurate bank reconciliation reports and financial data in the form of balance sheets, profit and loss statements, and cash flow statements.


Using their accounting knowledge and expertise in software, they can also forecast future revenues based on historical data. They may also project the financial ramifications of a financial decision before you make it.

Accounts Payable

Accounting pros can get third-party apps to work with the accounting software for more robust accounts payable management. Once this is set up, they can work on your invoice obligations and present it to you for approval.

Shopify Accounting Software Works Best With Unloop

Whatever software you acquire for your Shopify business, our team at Unloop can offer assistance. We primarily specialize in QuickBooks and Xero, but we can offer help if you want to transition to these two accounting software for more efficient financial recordkeeping.QuickBooks and Shopify ecommerce are our specialty. So if you choose to get QuickBooks for your online store, we'll be happy to help run your accounting software for you. Call us at 877-421-7270 for a consultation, or check out our ecommerce services now.

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About unloop

Unloop is the first and only accounting firm exclusively servicing ecommerce and inventory businesses in the US and Canada. With the power of people and technology, our team dives deep into COGS and inventory accounting.. You are paired with a dedicated bookkeeping team that prepares accurate financial statements, financial forecasts, and can also pay bills or run payroll for you. Come tax time, everything is organized and ready to go, so you don't need to worry. Book a call with an ecommerce accountant today to learn more.