Best accounting software for Shopify and Amazon sellers

Most UK Shopify and Amazon sellers need two things: accounting software that holds the ledger, and a connector that turns each marketplace payout into a summary journal of sales, fees, refunds and VAT. Xero, QuickBooks Online and FreeAgent are the usual ledgers; A2X and Link My Books are the usual connectors. Prices below come from each provider’s own pricing page, checked on 6 November 2026, and providers are listed alphabetically, not ranked.

Why do ecommerce sellers need a connector?

A connector is needed because a marketplace payout is not the same as your sales. Amazon and Shopify pay out a net figure after fees, refunds, chargebacks and sometimes tax. If you post only the bank deposit, your turnover is understated and your fees are missing.

A connector such as A2X or Link My Books reads the settlement report and posts one summary per payout. Each line goes to the right account: gross sales, marketplace fees, shipping, refunds and VAT. The summary then matches the bank deposit to the penny, so reconciliation is quick.

Bank feeds alone work only for very small sellers with a few orders a week.

Accounting software prices for online sellers

These are the published monthly prices ex VAT for the ledgers most often paired with ecommerce connectors.

Xero’s Ignite plan caps you at 20 invoices and 10 bills a month, which a growing shop can pass quickly. New Xero customers can get 90% off for the first 6 months with the offer on its pricing page. FreeAgent offers 50% off for the first 6 months and is free with a qualifying NatWest, Royal Bank of Scotland or Ulster Bank business account.

QuickBooks lists 1 user on Simple Start, 3 on Essentials, 5 on Plus and 25 on Advanced. Inventory tracking is listed on Plus and Advanced only. Its UK pricing page loads prices live, and they did not display when we checked, so confirm the figure with Intuit. See our Xero pricing and FreeAgent pricing guides for plan detail.

Connector prices: A2X and Link My Books

Both connectors price by sales channel and order volume rather than by user.

A2X shows starting prices in US dollars for Amazon, Shopify, eBay, Etsy, TikTok Shop and PayPal. Its homepage also names Sage as a supported platform. Higher order volumes cost more.

Link My Books does not print a fixed price list. Its calculator sets the fee from your rolling average monthly orders (tiers from 200 to 250,000) and the number of channels. It offers a 14-day free trial with no card and 90 days of history. It covers Amazon, Shopify, eBay, Etsy, TikTok Shop UK, WooCommerce and Square, and does not work with Xero’s Cashbook plan.

Which setup applies to you?

Use the volume and structure of your business to pick a starting point.

• If you sell only on Amazon as a sole trader, then FreeAgent with its £6 Amazon add-on, or a ledger plus one connector channel, keeps cost low.
• If you sell on Shopify and Amazon together, then you need a connector covering both channels, posting into Xero or QuickBooks Online.
• If you sell in euros or dollars, then you need a plan with multi-currency, such as Xero Comprehensive or QuickBooks Essentials.
• If you hold stock in several places, then you need inventory tracking in the ledger or a separate inventory tool.
• If your accountant already uses one ledger, then use the same one; it cuts their time and your fee.

What HMRC now sees about online sales

HMRC receives seller data directly from platforms. Since 1 January 2024, UK digital platform operators collect your name, home address, date of birth and National Insurance number, or a company’s registration number. They report your details and income to HMRC by 31 January after each calendar year.

Platforms do not report sellers with fewer than 30 sales of goods and under €2,000 (about £1,700) in the year. HMRC stresses that being reported does not automatically mean tax is due. Buying or making goods to sell for profit is likely to be trading; clearing out household items is unlikely to be.

Three thresholds matter for growing sellers:

• £1,000 trading allowance. Gross trading income over £1,000 means registering for Self Assessment.
• £90,000 VAT threshold. Count gross taxable sales over the last 12 months, not payouts. Track it with our VAT threshold tracker.
• Making Tax Digital for Income Tax. Sole traders with qualifying income over £50,000 joined on 6 April 2026; the threshold falls to £30,000 from 6 April 2027. See our Making Tax Digital hub.

What to do now

1. Download a year of settlement reports from each marketplace.
2. Compare gross sales with what you have recorded. Platform reports to HMRC show income after fees by quarter.
3. Pick one ledger and one connector, and use free trials before paying.
4. Map fees, refunds and VAT to separate accounts before the first sync.
5. Check your 12-month turnover against £90,000 every month.

Frequently asked questions

Can I use Shopify or Amazon reports instead of accounting software?

Marketplace reports are a source record, not a set of books. HMRC says the platform income report helps you track earnings but does not replace your business records.

Does A2X work with Sage?

A2X’s homepage names Sage as a supported platform, but its pricing page lists only QuickBooks Online, Xero and NetSuite. Check with A2X before you buy.

Do I count Amazon payouts or gross sales for VAT?

Count gross taxable sales. Marketplace fees are a cost to you and do not reduce turnover for the £90,000 VAT registration test.

Will HMRC know about my eBay or Etsy sales?

Yes, if you pass the reporting limits. Platforms report sellers with 30 or more sales of goods, or over €2,000, in a calendar year.

Which accounting software has a built-in Amazon link?

FreeAgent sells an Amazon add-on for UK Amazon Marketplace sellers at £6 a month ex VAT. Other ledgers rely on connectors such as A2X or Link My Books.