Industry specialists
Accountants for E-commerce & Online Sellers
At a glance
- UK VAT registration is compulsory at £90,000 taxable turnover — and marketplace fees from overseas platforms count via the reverse charge
- Since 2021, marketplaces collect VAT on many overseas-seller transactions — but UK sellers still account for their own domestic sales
- HMRC receives sales data directly from digital platforms (reporting rules live since January 2024) — undeclared selling income is visible
- Proper inventory (cost of goods sold) accounting is what makes e-commerce margins meaningful — cash-basis guesswork hides losses
- Typical fees: £83–£227/month for a VAT-registered e-commerce limited company on our benchmarks
Why marketplace sellers outgrow generalist accountants
An Amazon settlement isn't income — it's income minus FBA fees, advertising, refunds, and reserved balances, often spanning two VAT periods. Multiply by Shopify, eBay, Etsy, and TikTok Shop, add multi-currency, and manual bookkeeping collapses. Specialists wire each channel into Xero or QuickBooks through connectors (A2X, Link My Books, Dext Commerce) so every settlement splits into its components automatically — the difference between knowing your margin and guessing it.
VAT is where e-commerce gets expensive to get wrong
The rules differ by channel and customer location: domestic sales you handle normally; some cross-border marketplace sales the platform collects; EU consumer sales may need an IOSS or OSS registration; storing stock in an EU warehouse (Amazon FBA's Pan-EU programme) creates foreign VAT registrations immediately. A specialist maps your channels once and keeps you registered exactly where required — no more, no less.
The numbers that actually run the business
Good e-commerce accountants produce channel-level profitability — what you actually make per unit on Amazon versus your own site after fees, shipping, advertising, and returns. That drives stock decisions, pricing, and when to drop a channel. Expect monthly management figures, not just a year-end tax return: in a business where cash is tied up in stock, an annual snapshot is too late.
Frequently asked questions
I sell on the side — do I need to declare it?
Once total self-employed income passes the £1,000 trading allowance in a tax year you must register for self assessment. Platforms now report seller data to HMRC directly, so declare before HMRC writes to you — penalties are far lower.
Do I need special software for e-commerce accounting?
Xero or QuickBooks plus a settlement connector (A2X or Link My Books) is the standard stack. Most specialist accountants include the subscriptions in their monthly fee — ask before buying your own.
When should an online seller register for VAT?
At £90,000 rolling 12-month taxable turnover it's compulsory — but watch earlier triggers: overseas marketplace fees (reverse charge counts toward the threshold in some cases), EU stock storage, and voluntary registration to reclaim VAT on stock if your customers are businesses.
Information only — not tax, accountancy, or financial advice. Rules and thresholds change; confirm current positions with GOV.UK or a qualified accountant. Last reviewed: 2026-07-09.