The Best Accounting Software for Ecommerce Shops and How to Choose

When running an ecommerce business, you need accounting software that automates much of your accounting work. If you work with an accountant or partner with an accounting firm, you are likely using accounting software already.

But if you’re just starting your ecommerce business and looking for the ideal accounting software, there are several options available.

In this post, we compared the top ecommerce accounting solutions to help you make the right decision. 

What is ecommerce accounting software?

Ecommerce accounting software differs from regular accounting software. It encompass all ecommerce and online store-related matters to tax your business accordingly.

When choosing the right accounting software, it is wise to choose one that has features beneficial to ecommerce businesses.

How to lower your audit risk

Many challenges that ecommerce business owners face can be solved by choosing the right accounting software. Choosing the right solution comes down to comparing key features. 

Though you may think every accounting software has everything you need, you’ll be surprised that some basic features may not be included. Here are the top features to look for:

1. Platform integrations

Your accounting software should easily integrate with your ecommerce platform such as Squarespace, Shopify, BigCommerce, and WooCommerce.  Additionally, it should easily integrate with third-party tools, like contract management, employee expense management, and more.

With these integrations, you can automatically update your inventory levels, taxes, payments collected, and more. 

2. Comprehensive reports

Most major accounting softwares offer basic reporting. If your ecommerce business expects rapid growth, you will need  advanced reporting. You should get monthly, weekly reports — especially inventory reports. 

3. Sales tax configuration

As an online business, sales tax is very confusing. Your accounting software should make it as easy as possible to charge and account for sales tax.

4. 24/7 Support

24/7 support is necessary when your business’s backend accounting runs on a single application or software. It’s important to check out support ratings and reviews to see how a software companies’ customer support holds up.

The 7 best ecommerce accounting software picks of 2025

There are dozens of accounting software options available in 2025. Market leaders like QuickBooks and NetSuite continue to offer new features that simplify the business accounting process. 

Several new software companies, like FreeAgent and Wave, aim to change how SaaS accounting works to make it easy for any business owner to manage accounting efforts. 

1. QuickBooks

QuickBooks is the leading accounting software for small- and medium-sized businesses. It offer on-premises accounting applications and cloud-based versions with features like expense tracking, tracking bills and due dates, and reporting. 

With many features designed to support ecommerce businesses, you will find that QuickBooks has everything you need to properly track your inventory, taxes, expenses, and more. With native integrations available for major ecommerce platforms like Shopify and BigCommerce, QuickBooks should definitely be on your radar. 

QuickBooks Features

• Automatic Daily Sync: Quickly and easily import all your orders and refunds from your ecommerce platform into QuickBooks. You can choose to automatically sync order data and export historical data from your ecommerce platform’s account.
• Payments Support (Shopify Payments, PayPal, etc.): Automatically sync your payouts and fees with QuickBooks.
• Order Details: Each order you export from your ecommerce platform into QuickBooks will automatically include all line items, shipping, and taxes.
• Sync Product + Inventory Levels: Import products and inventory levels from Quickbooks Online into your ecommerce platform.

QuickBooks Pros

• Integrates with most ecommerce platforms
• Easy to use 
• Connects to all major accounts
• Simple pricing structure 
• Numerous reporting features and templates 

QuickBooks Cons

• Advanced features have a steep learning curve

Learn more about QuickBooks here.

2. FreeAgent

FreeAgent is a cloud-based accounting solution for small businesses owners to manage invoices, expenses, payroll, tax returns and other accounting tasks.

FreeAgent Features

• Estimates and invoices
• Expense, income, and profitability reporting
• Time tracking
• Reporting dashboard for taxes, expenses, and more
• Bank connections for transaction imports

FreeAgent Pros

• Easy to use 
• Free pricing plan available
• Regularly updates with new features
• Excellent tax reporting features

FreeAgent Cons

• Pricier than other competitors
• More template options needed
• Lack of 24/7 support

Learn more about FreeAgent here.

3. Wave Accounting

Wave is a web-based integrated accounting solution exclusively designed for small businesses. With the bank reconciliation feature, businesses can link their bank accounts, PayPal accounts, and other sources of data for real-time transaction records. 

Businesses can also generate reports such as balance sheets, sales tax reports, accounts receivable, and payable.

Wave Features

• Invoicing 
• Billing
• Payment tracking
• Payroll management
• Finance management
• Receipts

Wave Pros

• One of the most affordable options on the market 
• Competitive rates for credit card transaction processing and bank transfers
• Mobile apps available so you can always check your reports and accounts

Wave Cons

• Only uses accrual accounting with no support for cash-basis accounting
• Only has 12 base reports available, with no customization

Learn more about Wave Accounting here.

4. FreshBooks

FreshBooks Features

• Customizable invoices
• Payment reminders
• Automatic late fees
• Credit card processing
• Add discounts to invoices
• And more 

FreshBooks Pros

• Easy to use 
• Integrates with most ecommerce platforms
• Constantly updates with new features
• Detailed help articles for self-service support
• Simple pricing structure

FreshBooks Cons

• Limited inventory tracking
• Only supports single-entry accounting
• Reporting features are lacking when compared to other software

Learn more about FreshBooks here.

5. NetSuite

Designed for large enterprises, NetSuite cloud financials and accounting software helps finance leaders design, transform, and streamline their processes and operations. 

NetSuite combines core finance and accounting functions with strong compliance management. This combination improves business performance and increases financial close efficiency while reducing back-office costs. 

If you are running a large business with worldwide operations, NetSuite is worth checking out.

NetSuite Features

• Billing 
• Revenue recognition
• Planning and budgeting
• Global accounting
• Sales order management
• Returns management
• Inbound and outbound logistics

NetSuite Pros

• Leading software for large enterprises
• Offers many features not available with other accounting software
• Support for global accounting if you operate in multiple countries
• Offers compliance services to support ASC 606, GAAP, SOX, and others

NetSuite Cons

• Not a good solution for small- to medium-sized businesses due to pricing
• Multiple NetSuite software products are required if you want all their features

Learn more about NetSuite here.

6. Sage Accounting

Sage is a cloud-based accounting and invoice management solution for small businesses. It offers core accounting, project accounting, expense management, and compliance management all in one.

Sage manages all the documentation and processes required in business payments such as price quotes, estimates, statements and invoices. They offer integration with major banks, allowing users to import all payment transactions automatically. 

All information is available in a single dashboard, which allows users to stay up to date on their cash flow and pending payments.

Sage Accounting Features

• Inventory/stock management
• Bank reconciliation
• Automated billing
• Forecasting
• Pay bills electronically, print paper checks
• Supplier management

Sage Accounting Pros

• Easy to use 
• Connects to all major banks for automatic transaction updates
• Automates basic tasks including reconciliations
• Can email everything to customers to reduce physical paperwork
• Supports inventory and stock management tracking

Sage Accounting Cons

• Web app has less features than desktop app
• Occasionally slow even with a good internet connection
• If using the desktop app, you must create backups or you risk losing data

Learn more about Sage Accounting here.

7. Xero

Xero is a web-based accounting system designed for small and growing businesses. Xero connects small businesses with their trusted advisors and provides business owners with instant visibility of their financial position.

As a web-based solution, Xero can be accessed from any device with an active internet connection. With Xero’s robust accounting features, small businesses can view their cash flows, transactions, and account details from any location. 

Bank transactions are all automatically imported and coded. Online bill pay helps you keep track of spending and upcoming bills, improving relationships with the vendors that provide critical business materials.

Xero Features

• Inventory and stock management
• Bank reconciliation
• Contact database and segmentation
• Invoicing and payments
• Payroll
• Mobile apps available 

Xero Pros

• Affordable pricing
• Easy to use 
• Connects to all major banks
• Easy to view and customize reports

Xero Cons

• No phone support. Customer support is hrough email
• Support can take more than 24 hours to reply  
• Automatic reconciliation is occasionally incorrect, requiring you to manually review transactions 
• Needs more expanded user permissions for team members

Learn more about Xero here.

Conclusion

There are a lot of options available for ecommerce accounting software. Whether you’re deciding to use accounting software for the first time, or you’re looking to make a switch, you have great options available for your ecommerce business.

When choosing the right option, be sure to find one that aligns with your ecommerce business needs with features such as inventory accounting. 

Let the pros take care of inventory accounting

ShipBob’s software, including its inventory tracking features, enables automatic tracking of all your products.

Through integrations with major ecommerce platforms like Shopify, WooCommerce, Squarespace, or BigCommerce as well as other tools, you can automatically sync your inventory and get real-time updates. 

Even better, you don’t have to handle ecommerce fulfillment yourself. A 3PL partner like ShipBob provides ecommerce warehousing, technology, and the support you need to grow your ecommerce business.  

“I felt like I couldn’t grow until I moved to ShipBob. Our old 3PL was slowing us down. Now I am encouraged to sell more with them. My CPA even said to me, ‘thank god you switched to ShipBob. ShipBob provides me clarity and insight to help me make business decisions when I need it, along with responsive customer support.” 

Courtney Lee, founder of Prymal

To see if you’re a good fit and to get a pricing quote, click the button below.