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Best Accounting Software for E-commerce Businesses

Look for e-commerce accounting software that lets you process payments and track inventory and sales tax.
By Rosalie Murphy
Last updated on December 5, 2023
Edited bySally Lauckner
Fact checked and reviewed

⏰ Estimated read time: 7 minutes

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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.

Best Accounting Software for E-commerce Businesses

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QuickBooks Online

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on QuickBooks Online's secure website

5.0/5

Best for Overall e-commerce accounting software

$30/month

Additional pricing tiers (per month): $60, $90, $200.

50% off

for first three months or free 30-day trial.

Learn more

on QuickBooks Online's secure website

Xero

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on Xero's secure website

5.0/5

Best for E-commerce accounting software for multiple users

$15/month

Additional pricing tiers (per month): $42, $78.

30-day free trial

or monthly discount (terms vary).

Learn more

on Xero's secure website

Zoho Books

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on Zoho Books' secure website

4.5/5

Best for Best value e-commerce accounting software

$0

Additional pricing tiers (per month): $20, $50, $70, $150, $275.

14-day free trial

of the Premium plan.

Learn more

on Zoho Books' secure website

FreshBooks

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on FreshBooks' secure website

4.5/5

Best for Small service-based e-commerce businesses

$19/month

Additional pricing tiers (per month): $33, $60, custom.

30-day free trial

or monthly discount (terms vary).

Learn more

on FreshBooks' secure website

A2X

Best for Accounting software for e-commerce marketplaces

$19/month

Additional pricing tiers (per month): $69.

Free trial

Trial time is unlimited, but functionality is limited.

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.

QuickBooks Online

Learn more

on QuickBooks Online's secure website

Starting at
$30/month

Additional pricing tiers (per month): $60, $90, $200.

Promotion
50% off

for first three months or free 30-day trial.

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.

Learn more

on Xero's secure website

Starting at
$15/month

Additional pricing tiers (per month): $42, $78.

Promotion
30-day free trial

or monthly discount (terms vary).

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.

Zoho Books

Learn more

on Zoho Books' secure website

Starting at
$0

Additional pricing tiers (per month): $20, $50, $70, $150, $275.

Promotion
14-day free trial

of the Premium plan.

Our pick for

Small service-based e-commerce businesses

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

FreshBooks

Learn more

on FreshBooks' secure website

Starting at
$19/month

Additional pricing tiers (per month): $33, $60, custom.

Promotion
30-day free trial

or monthly discount (terms vary).

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.

A2X

Starting at
$19/month

Additional pricing tiers (per month): $69.

Promotion
Free trial

Trial time is unlimited, but functionality is limited.

Our picks for the best e-commerce accounting software

QuickBooks Online: Best overall accounting software for e-commerce businesses

Price:
  • $30 per month for the Simple Start plan.
  • $60 per month for the Essentials plan.
  • $90 per month for the Plus plan.
  • $200 per month for the Advanced plan.
Why we like it: QuickBooks is generally regarded as the industry standard in accounting software because it offers a wide variety of features and many accountants use it. A key differentiator for e-commerce businesses is that QuickBooks Online can automatically look up sales tax in each jurisdiction, then tell users how much they owe each sales tax authority and when payments are due. QuickBooks’ large app library also allows users to import Shopify and Etsy data and sync with a large number of sales platforms, making it an efficient option that should save business owners time. Read our full QuickBooks Online review.

Xero: Best e-commerce accounting software for multiple users

Price:
  • $15 per month for the Early plan.
  • $42 per month for the Growing plan.
  • $78 per month for the Established plan.
Why we like it: Every Xero plan allows unlimited users, so it could be a good option if you’re running your business with a team. Beyond that, Xero offers many features, including integrations with a large number of e-commerce platforms and inventory management programs. Xero can also calculate sales tax and generate a sales tax report, although it relies on a third-party app, Avalara, for automated sales tax functions. Read our review of Xero Accounting.

Zoho Books: Best value e-commerce accounting software

Price:
  • $0 per month for the Free plan.
  • $20 per month for the Standard plan.
  • $50 per month for the Professional plan.
  • $70 per month for the Premium plan.
  • $150 per month for the Elite plan.
  • $275 per month for the Ultimate plan.
Why we like it: Zoho Books (and its companion Zoho Inventory) is a good value as many of its features — including invoicing, accounting reports and the ability to manage 1099 contractors — are available for free to the smallest businesses. Zoho Books can generate a sales tax report and relies on Avalara for up-to-date sales tax rates. It can also manage inventory levels and send low stock alerts based on reorder points, but for full inventory management that integrates with online marketplaces, you’ll need Zoho Inventory. Read our complete Zoho Books review.

FreshBooks: Best for small service-based e-commerce businesses

Price:
  • $19 per month for the Lite plan.
  • $33 per month for the Plus plan.
  • $60 per month for the Premium plan.
  • Custom pricing for the Select plan.
Why we like it: If you’re a freelancer or solopreneur with a business that caters to clients and requires regular invoicing and collection of online payments, FreshBooks may be a great fit. It’s accounting software that’s particularly strong in invoicing, accepting online payments and tracking time and mileage. Therefore, it works well for small service-based businesses such as a boutique ad agency, tutoring business, cleaning service, pet sitting and dog walking and similar businesses for which you advertise, book, invoice and collect payment online. FreshBooks has its own payment processing offering with competitive transaction rates, and it also connects with Stripe and PayPal payment gateways to accept online payment from your clients.

A2X: Best accounting software for e-commerce marketplaces

Price:
  • $19 per month for QuickBooks or Xero integration with Amazon, Shopify, Etsy, eBay or BigCommerce.
  • $69 per month for QuickBooks or Xero integration with Walmart.
  • $79 to $199 per month for multichannel integration plans.
Why we like it: Think of A2X as the missing link between your e-commerce platform and accounting software. It automatically converts the raw data from your online sales channel reports into properly categorized transaction types that your accounting software can recognize and reconcile. Because it’s software that lives separately from your accounting solution and e-commerce platform, it comes with its own additional subscription cost. It’s an additional cost, however, that’s likely to pay off in reduced stress and human error when it comes to reconciling your reports, transactions and taxes.
Few direct integrations exist between popular accounting software and the major online selling channels, and those that do come with low user ratings and many negative reviews. This solution from A2X, however, receives hundreds of 5-star reviews for its ability to auto-sync sales data from platforms like eBay, Shopify, Etsy and BigCommerce with accounting software such as Xero and QuickBooks Online.

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. 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.

Does the accounting software integrate with your selling platform?

Whether your shop runs on Amazon, Shopify, WooCommerce, Etsy or elsewhere, your accounting software should be able to easily import data from your online shopping cart so you know how much revenue you’re generating.

Does the accounting software integrate with inventory management software?

Depending on how big your e-commerce business is, you may not package and ship every item yourself. Inventory management software can help you keep track of stock levels.
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.
Last updated on December 5, 2023

Methodology

NerdWallet’s accounting software ratings favor products that are easy to use, reasonably priced, have a robust feature set and can grow with your business. Ratings are based on weighted averages of scores in several categories, including range of features, cost, ease of use, accounting standards compliance, scalability, ease of sharing with accountants, integrations, customer support, pricing transparency and availability of a free trial period. Learn more about how we rate small-business accounting software.
These ratings are meant to provide clarity in the decision-making process, but what’s best for your business will depend on its size, growth trajectory and which features you need most. We encourage you to research and compare multiple accounting software products before choosing one.
NerdWallet does not receive compensation for any reviews. Read our editorial guidelines.
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