As an ecommerce entrepreneur, you need accounting software that has built-in automation tools, saving you hours of data entry time. In addition, accounting software for ecommerce should allow you to track and report on taxes, inventory, revenue, and fees. While many accounting software applications will work to track most of the information you need, there are some accounting solutions built specifically with the ecommerce entrepreneur in mind. Here are five of the best accounting software options for your ecommerce business.
Top 5 Ecommerce Accounting Software for Small Businesses
Ecommerce Accounting Software | Best For |
|---|---|
Best (overall) Ecommerce accounting software | |
Ecommerce businesses that don’t need to track their accounts payable | |
Businesses that need many users to access the software | |
Companies that need a free and simple solution | |
Ecommerce shops that want direct integrations with no third-party setups |
Accounting Software Integrations
There are not many accounting software solutions that are built specifically for ecommerce use. However, there are many integrations, add-ons, and plug-ins available for most accounting software packages that can automate, simplify, and streamline your accounting and bookkeeping processes. When you are evaluating accounting software, make sure to take into consideration any integrations your software may work with to make your life easier or provide functionality that does not come in your basic accounting software package.
QuickBooks Online: Best (Overall) Ecommerce Accounting Software
| Features We Like | What’s Missing |
Integration with common ecommerce tools | Vendor contract management | |
Tax tracking and reporting capabilities | Does not connect to all financial institutions | |
Purchase order and inventory tools | ecommerce tools are | |
Pricing
| ||
Features We Like | What’s Missing |
Integration with common ecommerce tools | Vendor contract management |
Tax tracking and reporting capabilities | Does not connect to all financial institutions |
Purchase order and inventory tools | ecommerce tools are |
Pricing:
| |
QuickBooks Online is ideal for any size ecommerce business. If all you need is basic bookkeeping features like tracking income and expenses, receipt capture and organization, quarterly tax estimates, invoicing and payment receipt, mileage tracking, and basic reports, you can go with the Self-Employed plan. If you need more than basic functionality, you can start with the Simple Start plan and upgrade as your business grows and expands. All plans include the ability to import sales data from major ecommerce websites like Shopify, WooCommerce, Magento, BigCommerce, and Volusion through the Intuit Marketplace integration apps. You can even sync sales and inventory between QuickBooks Online and Etsy, eBay, and Amazon with integrations or direct ecommerce connections.
FreshBooks: Best Ecommerce Accounting Software for Freelancers
 | Features We Like | What’s Missing |
Easy to set up and use | Lacks basic financial reports | |
Very good customer support | There are no accounts payable functions | |
Customizable invoices and online payment acceptance | No integrations available for Amazon or Etsy | |
Pricing
| ||
Features We Like | What’s Missing |
Easy to set up and use | Lacks basic financial reports |
Very good customer support | There are no accounts payable functions |
Customizable invoices and online payment acceptance | No integrations available for Amazon or Etsy |
Pricing:
| |
FreshBooks is ideal for ecommerce entrepreneurs who need easy-to-use accounting software that tracks their revenue and expenses and doesn’t take hours to produce useful reports. Although FreshBooks does not have accounts payable functions, it does have integrations available for Squarespace, Shopify, eBay, BigCommerce, and WooCommerce. The integrations offer various functions like syncing your sales and fees between your shop and FreshBooks.
Xero: Best QuickBooks Online Alternative for Ecommerce Businesses
 | Features We Like | What’s Missing |
Multicurrency options | Integrations with ecommerce apps may require tech skills | |
No limit on the number of users | Customer support can be difficult to get in contact with | |
Simple interface that is easy to use | No direct integrations with Amazon, Etsy, or Shopify | |
Pricing
| ||
Features We Like | What’s Missing |
Multi-currency options | Integrations with ecommerce apps may require tech skills |
No limit on the number of users | Customer support can be difficult to get ahold of |
Simple interface that is easy to use | No direct integrations with Amazon, Etsy, or Shopify |
Pricing:
| |
Connect your Xero account with point-of-sale (POS), inventory, and other integrations to complete your ecommerce accounting software solution. Bridge applications like Expandly and a2X allow you to connect Xero ecommerce platforms like Amazon and Etsy. Seamlessly sync your sales information to Xero and use their simple interface and navigation to perform all the financial tasks you need like running reports, paying bills, and invoicing customers.
Wave: Best Free Ecommerce Accounting Software
 | Features We Like | What’s Missing |
Easy tool for splitting transactions | No direct app integrations | |
Automatic categorization for bookkeeping transactions | No inventory management tools | |
User-friendly with great customer service | No accounts payable functions | |
Pricing
| ||
Features We Like | What’s Missing |
Easy tool for splitting transactions | No direct app integrations |
Automatic categorization for bookkeeping transactions | No inventory management tools |
User-friendly with great customer service | No accounts payable functions |
Pricing:
| |
Wave is the best free accounting software for ecommerce businesses. It’s also the only free accounting software on our list. It includes many of the features included in the paid software products with a few limitations. Inventory tracking and accounts payable are not available in Wave, and you can’t generate a cash flow statement. However, you can use Zapier to connect your Wave ecommerce accounting software to other applications like PayPal, DocuSign, Office 365, and more.
GoDaddy Bookkeeping: Best Ecommerce Accounting Software With Direct Integrations
| Features We Like | What’s Missing |
Direct integration capabilities | Limited reporting | |
Track mileage and time | No reconciliation functions | |
Mobile app with payment processing | Poor customer support | |
Pricing
| ||
Features We Like | What’s Missing |
Direct integration capabilities | Limited reporting |
Track mileage and time | No reconciliation functions |
Mobile app with payment processing | Poor customer support |
Pricing:
| |
GoDaddy Bookkeeping is one of the rare ecommerce accounting software solutions that was built with ecommerce sellers in mind. GoDaddy Bookkeeping provides built-in functionality for syncing your bookkeeping account automatically with Amazon, Etsy, eBay, or PayPal. The software can separate different fees and charges as expenses and apply your sales to the correct revenue classification when set up correctly, saving you tons of time when you’re preparing your taxes.
How We Evaluated Accounting Software for Ecommerce Businesses
We looked at several accounting software products and compared them based on cost, their ability to integrate with ecommerce websites, manage inventory, accept online payments, and other criteria.
Listed below are eight key areas we used to evaluate the best accounting software for ecommerce:
- Cost: The software should be affordable for any sized ecommerce business.
- Automates work: The solution should have some capabilities to automate basic entries to save the ecommerce entrepreneur time.
- Platform integrations: Solutions should allow you to connect your ecommerce accounting software to online selling platforms like Amazon, Shopify, Etsy, eBay, and more.
- Sync inventory: Inventory should sync between the selling platform and your ecommerce bookkeeping software to keep records accurate.
- Track and report on taxes: The software should allow you to set up your tax rates, track taxes by sales details, and produce a report that makes paying your taxes easy.
- Payment processing support: Payment processing should be an option with the software, allowing you to accept payments from customers easily.
- Track fees: Any fees paid to selling platforms or payment processors should be tracked as an expense and separated from the revenue by the software.
- Support: The software vendor should provide adequate support for an ecommerce business that may run during all hours of the day and night.
With these criteria and features in mind, we evaluated the five software solutions for ecommerce discussed in this article and chose the one we thought would work best.
Bottom Line
Whether you are just starting your ecommerce business or you’ve been in business for some time, there is a good accounting software package for you. It’s important to choose software that will save you time by automating many of the tedious data entry tasks that must be done with any ecommerce store. Remember to take into consideration which integrations and applications your accounting software can work with to create a total ecommerce accounting software solution.
We found that QuickBooks Online has affordable plans and includes key features like integration with many ecommerce websites and tools. QuickBooks Online also offers complete accounting and bookkeeping tools in addition to the ecommerce integrations that are capable with the software.
Anjali Gautam
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Amanda Norman
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