Selling via Amazon, eBay, Shopify or Etsy is set up technically in just a few minutes. Recording these sales cleanly for tax purposes is considerably more demanding. Each platform delivers its own reports, its own fee models and its own logic for payouts and cross-border deliveries. Those who do not work in a structured way from the outset risk incorrect VAT returns, incomplete bookings and unnecessary queries from the tax office.
Gross Payout Is Not the Same as Revenue
The most common mistake: the payout amount received in the bank account is booked as revenue. In reality, the marketplaces already offset their fees, refunds, advertising costs (e.g. Amazon Sponsored Products) and, in some cases, withheld VAT against the payout. What is decisive is always the gross revenue from the respective settlement report, not the net payment received.
Example: 10,000 euros in sales, less 1,500 euros in selling fees and 300 euros in advertising, results in a payout of 8,200 euros. For tax purposes, the 10,000 euros must be recorded as revenue and the 1,800 euros as an expense, kept separate, not the 8,200 euros net. Only then do the preliminary VAT return and the profit calculation add up correctly.
Platform Fees and the Reverse Charge Procedure
Amazon, eBay and Etsy regularly invoice their fees from another EU country (frequently Luxembourg or Ireland). The reverse charge procedure applies to these services: the German seller owes the VAT and reports it themselves, but at the same time deducts it again as input VAT. The prerequisite is that you have provided the platform with your VAT ID (USt-IdNr.). If this is missing, foreign VAT is charged, which cannot be deducted as input VAT in Germany.
Inventory Movements and the One-Stop-Shop Procedure
Particularly with Amazon FBA, goods are transferred to warehouses abroad (PAN-EU, CEE). These transfers are intra-Community transfers and trigger reporting obligations as well as, frequently, a VAT registration obligation in the country where the warehouse is located. For sales to private customers in other EU countries, the One-Stop-Shop procedure (OSS) has applied since the introduction of the EU-wide delivery threshold of 10,000 euros. Through it, you report centrally the VAT due in the respective country of destination.
Important: the OSS procedure only covers cross-border B2C shipping. Local sales made from a warehouse abroad must still be reported via a local registration. FBA sellers therefore generally cannot avoid a registration in the warehouse countries.
Keep Platform and Shop Cleanly Separated
Anyone selling in parallel via Shopify with their own payment service provider (e.g. Stripe, PayPal) and via marketplaces has different data sources. Shopify sales run through the payment service provider, marketplace sales through the respective reports. Both worlds must be recorded completely and without overlap, ideally via an interface that automatically transfers the reports into the accounting system.
Our Recommendation
- Archive reports: Download all settlement and fee reports every month and keep them in an audit-proof manner.
- Provide your VAT ID (USt-IdNr.): Check whether your VAT ID is entered correctly on every platform.
- Keep an eye on warehouse locations: Clarify the registration obligations before activating PAN-EU or CEE.
- Automate: Use a specialized interface instead of manual transfer.
E-commerce does not forgive blanket bookings. We support online sellers in recording marketplace and shop sales correctly from the start, setting up OSS and foreign registrations cleanly, and automating ongoing accounting. Talk to us before a structural error turns into a costly correction.