Accountants for e-commerce and online sellers

Selling online is deceptively hard to account for. Your sales live in five dashboards, your money arrives in different currencies on different days, your fees and refunds are buried in platform settlements, and your stock is somewhere between a supplier in China and an Amazon warehouse. The dashboard says you had a great month. Whether you actually made money, and whether you owe VAT, is a different question entirely. That’s the question we answer, clearly, every month.

Reviewed July 2026. E-commerce VAT rules change often and depend on how and where you sell. Always check GOV.UK or speak to us before acting.

What’s different about e-commerce accounting

Online retail breaks the normal rules of thumb. You often sell across several channels at once, each with its own fees, payouts and VAT treatment. Your “sales” figure is gross, before platform commission, payment fees, refunds, shipping and the cost of the goods, so the number on your screen is rarely your profit. Add cross-border sales, imports and marketplace VAT rules, and it’s a lot to keep straight. A generalist accountant who mostly does local trades tends to underestimate all of it. We do this every day.

The VAT trap: one threshold, all your channels

Here’s the mistake that catches growing sellers. The £90,000 VAT registration threshold applies to your total taxable sales across every channel combined, not per platform. So £40,000 on Amazon plus £30,000 on Etsy plus £25,000 on your Shopify store is £95,000, and you’re over the line, even though no single channel looks close. Cross it in any rolling 12-month period and you have 30 days to register. Miss it and HMRC can backdate the VAT, which for an online seller who never charged it can be a brutal bill. We watch your combined figure so it never sneaks up on you.

Marketplaces and VAT: who actually collects it?

This trips up almost everyone, because it depends on the platform. Amazon, eBay and Etsy act as the “deemed supplier” in certain cases and collect UK VAT for you, mainly on sales by overseas sellers and on low-value imported goods (£135 or less). Sell through your own Shopify site or website and there’s no marketplace in the middle, so you are the seller of record and account for the VAT yourself. And a crucial one for anyone using FBA: if you’re an overseas seller storing goods in a UK warehouse, the threshold is effectively zero and you must register before your first sale. We work out exactly which rules apply to your setup so you neither overpay nor get caught short.

Selling abroad: OSS, IOSS and imports

Once you ship overseas, a new layer appears. For B2C sales to EU consumers, the One Stop Shop (OSS) lets you report EU VAT through a single registration rather than in every country. For low-value goods (up to €150) sent to EU customers, the Import One Stop Shop (IOSS) lets you collect the VAT at checkout so parcels clear customs cleanly. On the way in, Postponed VAT Accounting lets you declare and reclaim import VAT on the same return instead of paying it at the border, which is a real cash-flow help. The rules here genuinely move (the EU is adding a small fixed customs charge on low-value parcels from July 2026), so this is exactly the area where specialist help pays for itself.

Getting your numbers right: settlements, fees and stock

The unglamorous heart of e-commerce accounting is reconciliation. Platform settlements lump together sales, commission, advertising, refunds and adjustments into one payout, and untangling them is the only way to see your true margin. Add stock and cost of goods sold, and “revenue” and “profit” can be worlds apart. We set you up on software that connects to your channels, reconcile it properly, and give you numbers you can actually make decisions on, like which products and channels are really making you money.

Making Tax Digital

Once you’re VAT-registered, you keep digital records and file through compatible software under Making Tax Digital for VAT. We handle the setup and the filing so it’s one less thing between you and your next order. Our VAT guide covers the essentials.

What we handle for you

On one fixed monthly fee: VAT registration and returns across all your channels, marketplace and cross-border VAT (OSS, IOSS, imports and PVA), multi-channel bookkeeping and settlement reconciliation, cost-of-goods and stock, your annual accounts and tax, and MTD. You get a dedicated accountant, our 3-hour email promise, and numbers in plain English, whether you’re a side-hustle Etsy maker or scaling on Amazon.

Why online sellers choose Xpert

Most sellers come to us either just past the VAT threshold and unsure what to do, or drowning in spreadsheets that never quite tie up. We’re proactive and e-commerce literate: fixed monthly fees, a real person who understands marketplaces and margins, no long tie-ins, and we handle the switch from your current accountant for you.

Selling online and want your numbers (and your VAT) under control? Take our 2-minute quiz or book a free consultation, and we’ll show you where you really stand.