Top 5 E-Commerce Accounting Software of 2023

With customers in many states — and maybe even around the world — online businesses need accounting software that supports their unique needs. The best e-commerce accounting software does that by offering built-in sales tax support and inventory tracking. If you choose software without those features, integrations with third-party inventory management and sales tax automation software are essential. These are our picks for the accounting software options best suited to online sellers.

Learn more about e-commerce accounting software here.

Our Picks for E-Commerce Accounting Software

Our Pick for Overall E-Commerce Accounting Software

QuickBooks Online stands out for e-commerce because it can automatically look up sales tax and tell you how much you owe and when it’s due.

Starting at $30/month
Additional pricing tiers (per month): $60, $90, $200
Promotion: 50% off for first three months or free 30-day trial

QuickBooks Online is an industry leader in the accounting field, thanks to its strong feature set, scalability, and ability to accommodate small businesses with more complex financial needs. With millions of users worldwide, your accountant will likely be familiar with it.

Pros

Easy to share information with your accountant and to find QuickBooks experts and online resources if needed.
More than 750 app integrations, including live, in-house bookkeeping.
Robust feature set includes thorough record-keeping, comprehensive reporting, excellent invoicing and inventory management, plus a capable mobile app.
Daily phone support and 24/7 chat support in all plans.

Cons

Expensive compared with the competition.
Limited account users with each plan.

Our Pick for E-Commerce Accounting Software for Multiple Users

Xero allows unlimited users, making it a good option for online businesses with big teams.

Starting at $15/month
Additional pricing tiers (per month): $42, $78
Promotion: 30-day free trial or monthly discount (terms vary)

Xero allows unlimited users at every subscription tier, a valuable feature for businesses where several users may need at least limited access to the system to run reports or analyze performance. Xero also has a customizable analytics dashboard that lets each user rearrange or hide panels.

Pros

Unlimited users in all pricing plans.
Integrates with more than 1,000 third-party apps.
Feature set includes an excellent mobile app and suite of reports, capable invoicing features, plus automated bill and receipt capture through Hubdoc.
Simple layout and easy to use.

Cons

No phone number for customer support listed.
Entry-level plan limits bills and invoices to five and 20 per month, respectively.

Our Pick for Best Value E-Commerce Accounting Software

Zoho Books is free for businesses with less than $50,000 in annual revenue, including access for one user and one accountant.

Starting at $0
Additional pricing tiers (per month): $20, $50, $70, $150, $275
Promotion: 14-day free trial of the Premium plan

Zoho Books packs an impressive collection of features and capabilities for an affordable price, and higher-tier plans let users automate workflows and track project profitability. It’s an especially good choice for users that already use the company’s other in-house apps and for businesses that want software with multilingual capabilities (Zoho Books supports 10 languages).

Pros

Less expensive than some competitors; free plan available for businesses with less than $50k in annual revenue.
Email support in free plan; phone and chat support in paid plans.
Rich feature set includes excellent invoicing, inventory management, workflow rules, and a capable mobile app.
Add accounting widgets to your phone’s home screen; track time using your Apple Watch.

Cons

Fewer third-party integrations and reports than some competitors.
No plan includes more than 15 users (can add additional users for a fee).

Our Pick for Small Service-Based E-Commerce Businesses

FreshBooks is accounting software that’s strong on invoice and online payment capabilities.

Starting at $17/month
Additional pricing tiers (per month): $30, $55, custom
Promotion: 30-day free trial or monthly discount (terms vary)

FreshBooks is a simple and affordable option for freelancers and very small businesses that don’t require many users and prioritize being able to operate on the go via a mobile app. It’s an especially inexpensive choice for those who can work within lower-tier plans’ billable client limits, and all plans include time tracking.

Pros

Stay in touch with clients through the FreshBooks mobile app and get notified when invoices have been viewed or become overdue.
Intuitive, customizable invoicing capabilities compete with those of more robust accounting solutions. Track time and add billable hours to invoices in all plans.
Weekday phone support in all plans.

Cons

Lacks features that quickly growing companies need, like audit trails for accountants to review.
Highest-tier Select plan only comes with two users (additional users add $11 per month) and lower-tier plans put limits on billable clients.

Our Pick for Accounting Software for E-Commerce Marketplaces

A2X is e-commerce accounting software for eBay sellers, those in search of Shopify accounting software, and any business that sells on an e-commerce platform.

Starting at $19/month
Additional pricing tiers (per month): $69
Promotion: Free trial
Trial time is unlimited, but functionality is limited.

A2X is a software integration that seamlessly flows your e-commerce financials into your accounting software for automatic transaction reconciliation, accurate reporting, and tax compliance.

Pros

Designed specifically for e-commerce accounting.
Highly rated integration to connect popular accounting software with your e-commerce marketplace.
Free trial lasts for an unlimited amount of time (although you’re limited to three payouts only and won’t get access to COGS).

Cons

Requires an additional monthly subscription to link your accounting software with your e-commerce shop.

Our Picks for the Best E-Commerce Accounting Software

When considering e-commerce accounting software, you’ll first want to make sure it works well with your selling platform and inventory management software. When these items can all talk to one another, it’s easier to stay on top of your finances.

Direct integrations between these systems are best because data can flow seamlessly from one to another, but highly rated ones that function well are hard to come by. Third-party integrations that connect your e-commerce and accounting software (for an additional subscription fee) abound — with much higher ratings and more positive reviews. Just make sure to test them, ideally during your software’s free trial period.

Also, if you work with a bookkeeper — which most business owners should at least consider — that person will need to access your books, ideally in real time.

How to Choose Accounting Software for Your E-Commerce Business

When considering e-commerce accounting software, you’ll first want to make sure it works well with your selling platform and inventory management software.

Does the accounting software integrate with your selling platform?
Does the accounting software integrate with inventory management software?

Your inventory software should communicate with all your selling channels to avoid mistakes, like selling products you don’t have in stock. It should also share data with your accounting software to help you understand how much capital is tied up in inventory and when you need to order more products.

How will you manage sales tax with your e-commerce accounting software?

When customers pay sales taxes, they pay the seller, not the government directly. The seller then has to pass those funds on to the city or state collecting them.

Because customers pay sales tax, rates are determined based on where they’re located, not where the seller is located. That’s easy for a brick-and-mortar store, since all of their in-person transactions happen in the same building. For an e-commerce business selling to customers all over the country or the world, it can get complicated.

E-commerce businesses need to keep track of how much sales tax they owe in each jurisdiction, then make tax payments.

QuickBooks Online automatically calculates sales tax based on the location of the customer, and QuickBooks users can generate sales tax reports so they know how much they owe to each jurisdiction.

Xero and Zoho Books both rely on Avalara, a third-party app, for tax calculations. Both of these programs can also generate sales tax reports.

If you choose a different software solution, make sure you know how to gather all the data your accountant needs.