5 Best Ecommerce Accounting Software

The Fit Small Business mission is to provide small business owners with the best answers to their small business questions. We evaluated our best ecommerce accounting software by conducting an in-depth internal case study where our experts determine the strengths and weaknesses of each platform.

There are only two scenarios where we may recommend a solution that has not been subjected to our case study—if the software is not a complete bookkeeping system or if we don’t have access to evaluate the program. We evaluated all the platforms in this guide on the same set of criteria regardless of whether it is a partner company.

QuickBooks Online offers a direct connection to your Shopify, Amazon, and eBay accounts in all of its plans, although the number allowed varies by plan.

• Simple Start: $35 per month for one user and one sales channel
• Essentials: $65 per month for three users and three sales channels
• Plus: $99 per month for five users and unlimited sales channels
• Advanced: $235 per month for 25 users

QuickBooks Online offers new customers the choice of 50% off for three months or a 30-day free trial.

QuickBooks Online is our overall best small business accounting software, and nowhere does it shine more than in ecommerce accounting. It has always led this category, but now it’s working hard to reduce the reliance on integrations to connect with your sales channels. We love that you can connect your Shopify, Amazon, and eBay sales channels directly from your QuickBooks Dashboard by clicking on “Commerce” in the left menu bar.

QuickBooks Online also doesn’t rely on an integration for advanced sales tax accounting. It will automatically determine the proper sales tax jurisdiction and tax rate based on the customer address in the invoice. All the other providers in this guide require an Avalara (or similar) integration for this advanced feature—save for Wave, which lacks the feature altogether.

While QuickBooks might seem a bit expensive at first, you’ll save money by needing to add fewer integrations than with other providers.

QuickBooks Online earned the highest overall score in our case study—thanks to its enhanced accounting features, such as invoicing and inventory management, and extensive ecommerce capabilities built into the base QuickBooks platform. For even more ecommerce options, you can integrate it with major ecommerce platforms, such as A2X, WooCommerce, Magento, and BigCommerce.

We also find QuickBooks excellent for mobile accounting. It allows you to complete various tasks, such as the ability to create and send invoices and accept payments from your smartphone. On the flip side, QuickBooks is less competitive in terms of pricing when compared with the other software on our list. Xero offers more affordable pricing—although you’ll need to do more work to set up ecommerce integrations.

All Xero plans include unlimited users:

• Xero Early: $20 per month for 20 invoices and five bills
• Xero Growing: $47 per month for unlimited invoices and bills
• Xero Established: $80 per month includes multiple currencies

Xero offers new users a choice between 75% off for three months or a 30-day free trial with no credit card required.

We recommend Xero for multiuser businesses because you can set up an unlimited number of users without any additional cost—unlike QuickBooks which is $235 per month if you need more than five users. It rivals QuickBooks in inventory, A/R, and A/P management, but it’s even better than QuickBooks in project accounting and fixed asset management.

We find Xero’s project accounting features especially beneficial for ecommerce businesses that offer made-to-order goods or operate on a project-based model. The software automatically calculates the costs associated with each job order and lets you generate quotes for customers. This feature can help you create competitive pricing for your customers.

For ecommerce businesses that use specialized equipment or machinery for production, you will appreciate Xero’s fixed asset management module. With it, you can accurately track your fixed assets, calculate depreciation, and manage disposals when needed. This means you can monitor the condition of your assets, which helps you plan for future replacements or upgrades.

Xero is nearly on par with QuickBooks in terms of accounting features, but its ecommerce integration capability is not as seamless as that in QuickBooks. You can’t connect any ecommerce sales channels directly from your dashboard, but Xero does have its own integrations with Zapier, Amazon, and Shopify. You’ll need a third-party connector like A2X or Parex Bridge to integrate it with other platforms, such as WooCommerce and Etsy.

Our case study also reveals that Xero’s biggest weakness is limited customer support options—explaining its poor score in ease of use. The provider offers support only through email, a chatbot, and some self-help guides. Other providers like QuickBooks Online and Zoho Books offer phone support which is crucial, especially for addressing integration and data syncing-related concerns.

Its mobile app is also not as functional as QuickBooks and Zoho Books, as it doesn’t allow you to accept payments from customers. Another significant drawback to Xero compared with QuickBooks is the relatively small number of independent bookkeepers available in the US to help you manage your books.

Sage 50’s monthly pricing is as follows:

• Pro: $60.08 for one user
• Premium: $103.92 for one user to $239.17 for five users
• Quantum: $177.17 for one user to $452.67 for 10 users plus custom pricing for more than 10 users

There is no free trial, but a Test Drive account that you can access by visiting Sage 50’s pricing page is available. It gives you full access to a cloud-hosted version of the Sage 50 desktop software, complete with sample data.

Sage 50 (formerly Sage 50cloud, which was formerly known as Peachtree) is one of the few remaining options for small businesses seeking desktop accounting software. QuickBooks Premier—the most popular small business desktop accounting software—is no longer available to new subscribers starting September 30, 2024. Sage 50 has been around for almost as long as QuickBooks and is more than capable of filling the gap left by the demise of Premier.

The downside of desktop software is the lack of integrations, but this is where Sage 50 surprised us. Sage 50 integrates with eBridge Connections, which then enables connections with Shopify, Amazon, eBay, Etsy, and more. It also integrates with Avalara to enable advanced sales tax management across all 50 states.

As expected, Sage 50 did great in our evaluation of accounting and inventory features. It has our A/R, A/P, and reporting features. It scored slightly behind Quickbooks Online in banking and cash management because of the lack of flexibility in handling bank deposits, which can result in a more complicated bank reconciliation.

While we think Sage 50’s ecommerce integrations are outstanding for a desktop program, it did score well behind QuickBooks Online and Xero in this category. Whereas Sage 50 is dependent on eBridge Connections for all its Ecommerce integrations, QuickBooks and Xero offer simpler-to-use direct connections and native integrations.

The major shortcoming of Sage 50 in our case study is its mobile app, which isn’t surprising given it’s a desktop program. Zoho Books has the best mobile accounting app we’ve seen and provides all the same accounting features as its computer interface.

• Free: $0 per month for one user and accountant for companies with annual revenues of $50,000 and below
• Standard: $20 per month for three users and 500 customers and vendors
• Professional: $50 per month for up to five users
• Premium: $70 per month for up to 10 users
• Elite: $150 per month for up to 10 users and advanced inventory control (recommended for Ecommerce businesses)
• Ultimate: $275 per month for up to 15 users, 25 custom modules, and advanced analytics

We are particularly impressed with Zoho Books’ strong mobile accounting features. This is important and timely for modern ecommerce businesses, especially those that need to track sales and inventory levels and manage orders away from their computers.

Zoho Books’ app beats even QuickBooks Online because it allows you to perform multiple tasks, such as sending invoices, accepting payments, and managing your expenses. This is why Zoho Books leads our roundup of the best mobile accounting apps.

What’s more, Zoho Books excels in inventory management. When you add Zoho Inventory, you can accurately account for inventory costs in the books and manage inventory requirements and reorder points. Plus, Zoho Inventory integrates with Amazon, eBay, and Etsy.

As one of our best bookkeeping software for ecommerce businesses, Zoho Books has remarkable accounting features like QuickBooks and Xero. However, it offers a free plan for very small businesses and excels in mobile accounting. It earned a perfect score in mobile accounting because it offers all of the features we wanted to see in a mobile app, including receipt capture, invoicing, and payment processing.

However, it took a hit in ecommerce integration due to its lack of built-in integrations unless you spend $150 per month for the Elite plan. Without the Elite plan, you’ll need to use Zapier or purchase additional Zoho products with their own Ecommerce integrations, such as Zoho Inventory, which ranges from $0 to $329 monthly, or Zoho Flows, which ranges from $12 to $30 monthly.

Zoho Books has plenty of options for customer support, but unlike Sage 50, customer support is unavailable 24 hours per day. It’s also not as easy to use as QuickBooks Online. Zoho Books is a bit complicated and can be overwhelming for some ecommerce business owners with no accounting background.

• Starter: Free; includes one user and most accounting and invoicing features
• Pro: $16 per month when billed monthly or $170 per year when billed annually; includes unlimited user access, bank connections, and unlimited receipt scanning

We included a free option for companies that are just getting started and not quite ready to make an accounting software commitment. While we don’t recommend Wave as a long-term solution for ecommerce companies, we do believe it is the best fit among free software. It has solid accounting and invoicing features along with a Zapier integration.

While more work than pre-built integrations, you don’t need to start your Zaps from scratch—there are already Zaps built that you can use for many processes. For instance, there are Shopify/Wave Zaps available on Zapier for recording Shopify sales, creating invoices in Wave from orders in Shopify, creating Wave customers from new Shopify orders, and more. The big drawback with Zapier is you need to create a new Zap for each action.

Wave leads in pricing, as it offers a free plan for a single user and a plan for unlimited users for just $16 per month. You can send unlimited invoices to customers and keep track of your accounts at no cost—making it our best free accounting software. Wave also did well in ease of use and user reviews. However, Wave scored poorly in most other categories compared with the higher-priced software in this guide.

The program lacks inventory accounting, and any ecommerce integrations must be accomplished by creating Zaps with Zapier—which is very time-consuming compared with the direct ecommerce integrations offered by other software. The program itself is simple and easy to use, but we had to deduct some points because of its limited customer support options, particularly in the free plan. You can only access email support and live chat when you purchase a paid add-on or upgrade to the paid version.

Using accounting software for ecommerce provides numerous benefits, including the ability to:

• Integrate with ecommerce platforms, such as Shopify, Amazon, WooCommerce, and BigCommerce
• Manage your financial transactions, such as sales, expenses, and taxes, efficiently
• Track inventory levels in real time and calculate COGS automatically
• Categorize and track expenses so that you’ll know where your money is going
• Perform automatic sales tax calculations for easier tax reporting and compliance
• Generate reports, such as profit and loss (P&L), cash flow statements, and sales tax reports