E-commerce Accounting for marketplace sellers.
Amazon and Shopify deposit a single figure after taking out fees, refunds and VAT. If you book that as sales, every number downstream is wrong. Here is how to get your accounts right.
The net-payout problem
Amazon and Shopify deposit a single figure with fees, refunds, and VAT already baked in. Book it as "sales" and every downstream number is wrong.
Jump to section 02API unpacking
Link My Books or A2X bridges break each payout into gross sales, individual fees, and VAT, turning opaque deposits into clean journal entries.
Jump to section 03Multi-channel VAT
The £90k threshold aggregates across every platform and your own site. International FBA can drag in overseas VAT registrations.
Jump to section 04Landed cost accuracy
Post-Brexit customs duty and import VAT treatment decide whether your margin calculation is real or fiction. Errors compound across every SKU.
Jump to sectionHow net payouts work
Marketplaces deposit a single "Net Payout" into your bank account. This figure has already had seller fees, shipping costs, refunds, and promotional charges deducted. If you record this deposit as your sales figure, your accounts are immediately wrong: revenue is understated, expenses are hidden, VAT is miscalculated, and you cannot see what each platform is costing you.
Solving this requires API bridges (such as Link My Books or A2X) that connect your marketplace accounts directly to your accounting software. These tools unpack every payout into its component parts (gross sales, individual fees, refunds, and VAT) and post accurate journal entries automatically.
Key Challenges for E-commerce Sellers
- Channel profit: Platform fees, FBA charges, and advertising costs must be tracked per channel to understand real margin.
- Multi-channel VAT: Selling across multiple platforms and your own website means aggregating turnover for VAT threshold purposes. International FBA can trigger overseas VAT obligations.
- Landed costs: Post-Brexit, importing goods to sell in the UK requires correct customs duty and import VAT treatment. Errors here compound through every SKU and the whole margin calculation.
Go Deeper
E-commerce VAT & Marketplace Accounting Guide 2026
How VAT and marketplace accounting work for online sellers, including deemed supplier rules, payout reconciliation and VAT return records.
GuideInventory & COGS Accounting for E-commerce
How e-commerce sellers record inventory and cost of goods sold, including opening stock, closing stock, landed costs and marketplace records.
GuideMarketplace Fees and True Profit for Sellers
How marketplace fees, shipping, refunds, stock and VAT affect true profit for e-commerce sellers using Amazon, eBay or Shopify.
GuideMulti-Channel Reconciliation for E-commerce
How to reconcile sales across Amazon, Shopify, eBay and payment processors so payouts, fees, refunds and VAT are recorded correctly.
GuideOSS & IOSS VAT for UK E-commerce Sellers
How OSS and IOSS VAT rules affect UK e-commerce sellers making EU sales, including thresholds, marketplace rules and record keeping.
Related Services
See your real net payout, marketplace fees and VAT in one view.
We connect your marketplaces, Amazon, eBay, Shopify, Etsy, into clean regular reporting, separate marketplace-collected VAT from your own obligations, and show the per-channel margin you are making.
Check your marketplace numbers