Top Shopify Accounting Solutions for 2025

Introduction 

Opening a store on Shopify can often feel like a great adventure. There are many big decisions, including which products to sell, how to attract customers, and how to fulfill the orders. 

Those are all essential questions to answer. And how well you answer them will have a direct effect on the success of your business. But there is more to running an effective DTC brand. You also need proper financial management to ensure profitability and regulatory compliance. 

The Shopify platform offers excellent tools for displaying and selling your merchandise. But its built-in features fall short of what you need to manage your bookkeeping and accounting. 

You need specialized Shopify accounting software, purpose-built to provide real-time visibility of your cash flow, automation to save time and eliminate errors, and simplified ways to manage your merchandise and give you real-time insights.  

This guide examines the best eCommerce accounting software options for Shopify sellers, including their features, pros, cons, and how to choose the ideal solution for your business needs and for your eCommerce accounting.

Why Shopify Sellers Need Accounting Software

Manual vs. Automated Accounting

Many eCommerce entrepreneurs start their Shopify journey by tracking their financial data manually on spreadsheets. This method might work in the early days of a business, but as the business expands, it becomes unsustainable. You really just need a better solution.

Manual systems are: 

• Time consuming
• Prone to error
• Hard to scale
• Unreliable for audits and tax calculations

You can avoid all these problems with a real-time accounting system. Automation saves time, eliminates errors, scales easily, and provides reliable data when you need it. 

Benefits of Using Accounting Software for Shopify

Time-Saving Automation

Say goodbye to manual reconciliation with Shopify bookkeeping apps. Track your orders and payments, and categorize expenses automatically. 

Accurate financial reporting

See your profit-and-loss statement, balance sheet, and cash flow statement in real time so you can always make informed financial decisions. 

Better inventory tracking

Stay on top of the real cost of your merchandise with real-time COGS reporting and full visibility of your merchandise levels in every warehouse. 

Simplified tax calculations 

Keep your financials updated and tax-ready so they are ready to go to your tax CPA.

Key Features to Look for in Shopify Accounting Software

Bank and Shopify Payment Reconciliation

Effective Shopify accounting software will automatically match transactions from your Shopify store, your bank accounts and your payment processors with your sales and expense records, ensuring all financial data is accurate and up-to-date.

Multi-Currency Support

Shopify sellers that operate globally need accounting software that can support multiple currencies. Ideally, the software would track revenue and expenses in different currencies while maintaining visibility of your financial reports in your home currency.

Integration with Tax Platforms

The ability to connect with specialized tax software or services is crucial for an eCommerce business. As DTC brands grow, they deal with complex sales tax requirements across multiple jurisdictions.

Best Accounting Software for Shopify Store Owners

Finaloop

Overview

Finaloop provides real-time financial tracking and seamless Shopify integration. It stands out as an accounting software plus service, specifically designed for eCommerce. Unlike general-purpose accounting software, Finaloop understands the unique challenges of online retail. 

Pros

• Built specifically for e-commerce with Shopify (and other platforms) -optimized workflows
• Real-time financial dashboards with eCommerce metrics
• Comprehensive integration with Shopify, payment processors, and banks
• Automatic reconciliation of Shopify payouts
• Accurate COGS and inventory valuation tracking

Cons

• Not suitable for non-eCommerce sellers such as traditional retailers.
• If you like spending tens of hours on your books every month, you will lose this pleasure.

QuickBooks Online

Overview

Quickbooks was created before eCommerce gained popularity, and its functions are well-suited for service-based businesses. It provides a range of general-purpose accounting capabilities, including invoicing, expense tracking, and financial reporting, though not specifically tailored for eCommerce. 

Pros

• Comprehensive accounting features and reporting tools
• Wide availability of accountants familiar with the platform
• Scalable plans for growing businesses

Cons

• Requires additional apps or connectors for full Shopify integration and a bookkeeper/DIY to manage
• Not specifically designed for e-commerce accounting workflows
• It can be complex for beginners with limited accounting knowledge

Xero

Overview

Xero is a cloud-based accounting solution designed for small businesses and sole traders. It offers a clean interface and allows an unlimited number of users for easy collaboration.

Pros

• Intuitive interface with minimal accounting jargon
• Unlimited users on all plans
• API for custom integrations

Cons

• General accounting platform, not specifically oriented to eCommerce
• Shopify integration requires third-party connectors
• Requires additional bookkeeper or DIY

FreshBooks

Overview 

FreshBooks is known for its user-friendly interface and strong invoicing capabilities, making it useful for non-accountants. The software is particularly well-suited for service-based businesses that need to track time and expenses for projects. 

Pros

• Easy to use and simple to navigate
• Strong invoice and payment processing features
• Time-tracking tools that allow users to log hours and convert them into invoices automatically

Cons

• Requires third-party apps for comprehensive Shopify integration
• Reporting features are less extensive than specialized e-commerce solutions
• Inventory management tools offer basic features but are not as robust as competitors

Shopify Accounting Apps to Enhance Bookkeeping

A2X for automation

A2X is a data transfer tool that specializes in automating the reconciliation of Shopify payouts with your accounting software. It ensures that your Shopify sales, fees, and payouts are correctly recorded in your accounting system. 

A2X can break down Shopify payouts into sales, fees, and taxes and post summary transactions to your accounting software. But it doesn’t offer financial reporting, reconciliation, or inventory management. And it isn’t always real-time. 

TaxJar for Sales Tax

TaxJar is a cloud-based sales tax solution that integrates with Shopify and your accounting software to automate sales tax compliance. It covers all tax jurisdictions across the US and provides detailed tax reports for each area. 

TaxJar supports product-specific tax codes so that the taxes collected are accurate for a wide range of goods and services. It can automate your tax reporting and assist with tax filing. 

Finaloop for Complete Integration

Finaloop is a full-service eCommerce accounting platform with a comprehensive solution and includes a team of top-notch accountants in the backend. It features real-time bookkeeping, COGs tracking, and inventory management. It offers automated payout reconciliation and tax-ready books, through native integrations.  

Finaloop was designed especially for DTC brands with no bookkeeper - all through a single system. 

How to Choose the Right Accounting Software for Shopify Sellers

Factors to consider when selecting accounting tools 

Business size and transaction volume

Businesses at different stages of their growth have different accounting needs. While there is always a need for real-time financial data and effective monitoring of COGS, early-stage DTC brands may be better off with simple bookkeeping software for their Shopify stores (some even start with spreadsheets). 

As their sales volume grows, DTC founders may find that their accounting needs grow in complexity, and they need a more sophisticated solution, especially one designed for eCommerce, which has accounting needs that general-practice retail software may not support.  

Reporting and Automation Needs

Consider the financial reports you need when you’re running a DTC company on Shopify. 

1. Profit and Loss reports - Knowing your profits and expenses in real-time is the basis of informed decision-making. If you only know your revenue figures but not how much you spent to get there, you may be operating at a loss and not know it. 
2. Cash flow reports - If you don’t know exactly how your cash is flowing through your operation, you might be spending too much at the wrong time. Alternatively, you might have more cash available than you realize, and you’re missing opportunities to order more merchandise to acquire new customers. 
3. Balance sheet reports - These reports provide a clear picture of the overall health of your company by indicating your real assets, liabilities, and equity. 
4. Inventory - With real-time inventory tracking, you can optimize your inventory management and avoid stockouts, which often become lost sales, and overstock, which costs you more in storage fees and ties up cash in merchandise that isn’t moving. 
5. COGS - To truly get a handle on your inventory management, you need real-time reports on the real costs of the goods you’re selling. 

For all these reports to be accurate in real time, the data has to be drawing directly from your accounts as an integrated whole. And the more advanced your reporting needs, the more important it is to choose software with eCommerce-specific capabilities.

Integration with Payment Processors

The best Shopify accounting software will have native integrations with all of the payment processors you’re using or plan to use in the future. 

While some software options require 3rd party integrators to collect the essential data, you are better off with a single system that can connect the entire payment and provide real-time financial reports.  

Cloud-based vs. desktop accounting software

Security, accessibility, and scalability

Modern eCommerce brands benefit more from cloud-based accounting solutions. A cloud-based system can be accessed from anywhere by any number of people, allowing for collaboration without being limited by geography. 

Cloud-based systems are more secure, and you don’t have to update your hardware whenever there is an upgrade in the security system. It happens automatically through the cloud. There is also more protection against data loss because most cloud providers offer strong backup protocols. 

They are also easier to scale, which is a major consideration for any eCommerce business. 

Future Trends in Shopify Accounting Software

AI and automation in eCommerce accounting

As automation technology continues to improve in Shopify accounting software and AI is more fully integrated into the process, it’s likely that the software will grow quicker, more accurate, and better able to detect potential errors before they happen by spotting unusual patterns (along with human overview). 

Growth of real-time financial analytics

It is already apparent that there is no substitute for real-time visibility of key financial data. Finaloop remains the only integrated Shopify accounting software that offers real-time financials, real-time data on inventory, providing up-to-the-minute reports on COGS and inventory. 

Enhanced automation for tax compliance

As tax regulations for eCommerce continue to grow in complexity, automation technology will evolve along with it to provide a range of new functions, such as; 

• Automated multi-jurisdictional tax calculation and filing
• Compliance monitoring
• Documentation management for audits

Final Thoughts: Choosing the Best Accounting Software for Shopify Sellers

Recap of Top Software Recommendations

While all the solutions we've covered offer valuable features for Shopify sellers, the best choice depends on your specific business needs:

• Finaloop stands out for businesses seeking a complete e-commerce accounting solution with minimal manual work
• QuickBooks Online is an option for businesses looking for a well-established platform with broad accountant familiarity
• Xero offers a user-friendly alternative with strong multi-user capabilities
• FreshBooks works well for Shopify sellers who also offer services alongside products

How the right software supports business growth

Investing in appropriate accounting software is one of the best ways to fast-track the growth of your business. You need clear financial visibility to make good business decisions, ones that will keep the company moving in a positive direction. For Shopify sellers seeking a purpose-built accounting solution, Finaloop offers the most complete solution on the market- check it out. 

FAQ

Does Shopify Come with Accounting Software?

Shopify provides basic financial reporting, such as sales reports through its dashboard. But it lacks the comprehensive real-time reporting companies need to see the whole financial picture. A DTC company looking to gain real insight from its financials will want to invest in more robust Shopify accounting software

Which Accounting Software is Best for Shopify?

The best accounting software for Shopify depends on your business needs:

• Finaloop is ideal for dedicated e-commerce businesses looking for real-time financial reports. 
• QuickBooks Online works well for businesses seeking a well-known brand, though one that isn’t designed especially for eCommerce. 
• Xero is a good choice for companies with collaborative teams and international sellers
• FreshBooks suits businesses offering both products and invoice services

For most growing Shopify businesses, solutions with e-commerce-specific features like Finaloop provide the most value.

Can You Do Accounting on Shopify?

While Shopify provides basic financial reporting, it's not designed to handle complete accounting functions. Shopify lacks essential accounting features such as:

• Balance sheets and proper financial statements
• Tax preparation capabilities
• Bank reconciliation