Accounting Software for Ecommerce: 10 Tools for Sellers

Ecommerce accounts are deceptively hard. One payout can hide hundreds of orders, refunds, fees and taxes, and the number that lands in your bank never matches the sales you made.

The ten tools below are listed alphabetically and in no particular order, and every description comes from the tool's own website, read this week. If you're working on growth too, there's a guide to conversion benchmarks for Shopify stores that helps you read your numbers.

Ecommerce accounting software compared

In the free plan column, Yes means the tool's own site names a free plan, a free version, a free account, a free allowance or open source software. Trial only means a time-limited trial. Not stated means the pages I read named neither, even where there's a button inviting you to start for free.

Tool	Type	Good for	Free plan
A2X	Ecommerce accounting software for sellers and accountants	Matching payouts to sales	Not stated
Bookkeep	Accounting automation for Shopify	Faster month-end for online brands	Trial only
Finaloop	Ecommerce accounting services, inventory and analytics	Done-for-you ecommerce books	Not stated
Link My Books	Bookkeeping links for Amazon, eBay, Shopify and Etsy	UK sellers with VAT to track	Trial only
Puzzle	AI accounting software and services	Startups wanting AI books	Trial only
Sage	Accounting software for small businesses	Sellers with a Sage accountant	Not stated
Synder	Accounting automation for online sales	Syncing payments from many platforms	Not stated
Taxomate	Ecommerce accounting for Amazon and Shopify	Amazon sellers watching profit	Not stated
Webgility	Ecommerce accounting and inventory automation	Inventory and accounting in sync	Not stated
Zoho Books	Online accounting software	Sellers already on Zoho	Trial only

Ten accounting tools for ecommerce sellers

A2X

Best for: Amazon and Shopify sellers who want payouts broken down into clean summaries for QuickBooks or Xero.

Bookkeep

Best for: Shopify brands that want daily sales journals posted automatically so the month-end close is quicker.

Finaloop

Best for: Direct-to-consumer brands that want ecommerce bookkeeping, inventory costing and analytics handled for them each month.

Link My Books

Best for: UK multi-channel sellers who want sales from several channels posted to Xero or QuickBooks with VAT handled.

Puzzle

Best for: Online startups that want AI accounting software with optional bookkeeping services, on a 14-day trial.

Sage

Best for: Established sellers whose accountant prefers this long-standing brand and wants standard accounting connected to their ecommerce channels.

Synder

Best for: Sellers taking payments through several platforms who want every transaction synced to their books.

Taxomate

Best for: Amazon sellers who want settlements posted to their books plus free fee and profit tools.

Webgility

Best for: Growing stores that want orders, inventory and accounting kept in sync in real time.

Zoho Books

Best for: Small online businesses using other Zoho apps that want accounting connected to their store and CRM.

Selling platforms now report to HMRC

This one catches UK sellers out. HM Revenue and Customs (HMRC) guidance says that if you're in the UK and run a digital platform that lets users sell goods or services, you need to check if you need to tell HMRC about sellers on your platform.

In practice, the platforms you sell on may be sending information about your sales to HMRC. That's another reason to keep accurate books that match what each platform reports, so there are no surprises if HMRC asks questions.

Connector or full bookkeeping platform?

Connectors sit between your sales channels and your accounting software. They break each payout into sales, fees, refunds and taxes, then post a tidy summary so your books match your bank.

Full ecommerce bookkeeping platforms and services go further, handling inventory costing, reconciliation and month-end for you. They suit busy brands that would rather not touch the books at all.

Getting your ecommerce books in order

List every channel you sell on and every way money reaches you, including payment processors. Most messy books come from one forgotten channel that nobody connected.

Then decide how you'll treat inventory, because what each item takes to make or buy is where ecommerce profit really shows. My guide to bookkeeping software for small business covers the general accounting side.

It's also smart to close each month within a week or two of it ending. Small mismatches are easy to fix when the sales are fresh in your mind, and they're a nightmare to untangle a year later when you're trying to file.

Questions to ask before you choose ecommerce accounting software

1. Does it connect to every channel I sell on?
2. Does it break payouts into sales, fees and refunds?
3. Does it handle VAT or sales tax for my countries?
4. Can it track inventory and the true value of stock sold?
5. Does it post to the accounting software I already use?
6. Will my accountant be able to review it easily?

Signs your ecommerce books need help

• Payouts never match sales. Reconcile each one.
• Fees are a mystery. Record them separately.
• You can't see profit by product. Track stock value.
• Month-end takes a week. Automate the sync.

Do you make accounting software for ecommerce? Tool makers can ask to be considered for a featured place on this list.

My plain advice on choosing accounting software for ecommerce

Get your payouts reconciling first and worry about fancy dashboards later. If your books match your bank every month, you'll know your real profit and sleep better at tax time.

And talk to an accountant who understands ecommerce. The right tool plus someone who knows how selling platforms pay out is worth far more than either on its own.

Frequently asked questions

What is the best accounting software for ecommerce?

It depends on your channels and whether you want a connector or a full service. The list above is in no particular order.

Do I need special software for Shopify or Amazon?

General accounting software works, but ecommerce tools make payouts, fees and refunds far easier to record.

Do selling platforms report to HMRC?

HMRC says UK digital platforms that let users sell goods or services need to check if they must tell HMRC about sellers.

What is a payout reconciliation?

It's matching each payout to the sales, fees, refunds and taxes it contains, so your books match your bank.

Are there free trials for ecommerce accounting tools?

Several offer trials. The free plan column shows what each tool's own site says.

Should I track inventory in my accounts?

Yes, if you hold stock. It's how you see your real profit on each sale.