Digital Tax Service · Guidance

Accounting and tax for an ecommerce company

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Ecommerce limited company accounting and VAT across sales channels, in navy and gold

Why ecommerce accounts are harder

  • Stock: you must value inventory and match sales to cost of sales — profit isn’t just income minus purchases
  • Volume: thousands of small orders, fees and refunds across Amazon, eBay, Etsy, Shopify and more
  • Fees and payouts: marketplace fees, payment-processor deductions and settlement timing all have to be untangled
  • VAT: marketplace collection, imports, and cross-border rules layered on top

Multi-channel bookkeeping

VAT for online sellers

VAT is where online sellers most often go wrong. Online marketplaces are frequently responsible for collecting VAT on certain sales — especially goods sold by overseas sellers or imported below set values — while your own registration depends on where you, your stock and your customers are. The UK £90,000 threshold still applies, but volume selling reaches it quickly.

When to register for VAT

Selling into the EU and beyond

Shipping goods to EU consumers can create EU VAT obligations. Schemes like IOSS (low-value imports) and OSS let you account for EU VAT centrally rather than registering country by country — but they must be set up correctly. Cross-border VAT is the single most expensive thing to get wrong as an online business scales.

What your ecommerce company files

The standard company obligations — annual accounts and a confirmation statement at Companies House, a CT600 with HMRC, VAT returns under Making Tax Digital, and payroll if you have staff. With clean multi-channel records behind them, none of it needs to be painful. We handle the lot. Call 0114 327 1480.

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Frequently asked questions

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