Amazon FBA & Multi‑Marketplace Accounting 2025: The Complete Guide for Online Sellers

If you sell via Amazon FBA, your own online shop, or across multiple marketplaces, your 2025 accounting comes down to three continuous challenges: mastering cash flows, mapping taxes correctly, and managing invoices compliantly. What seems like admin—payouts, fees, ads, refunds, vouchers, credits—decides your margin, compliance and peace of mind. This guide shows how online sellers can bring their Amazon accounting under control without drowning in CSV chaos.

1) Understanding transactions instead of merely posting them

On Amazon, Shopify & co, a sale rarely consists of one simple booking. It breaks down into gross sales, discounts, VAT, shipping, marketplace fees, advertising costs, refunds and sometimes currency effects. Only the payout hits the bank—net of all these elements. Unless you decompose and reconnect them, you book blindly, risking errors in VAT, profit reporting, and later audits.

The 2025 approach is transaction matching: every payment is matched with structured order, fee and refund data, so that journal entries mirror reality—regardless of whether you have 100 or 100,000 orders per month and whatever accounting software your tax advisor uses.

2) Fees, advertising and returns: make your margins honest

In Amazon FBA, fulfillment, sales and storage fees gradually erode margins. The same applies to advertising (PPC), payment processor fees or middleware charges in larger setups. Solid accounting maps these per order rather than aggregating monthly. This allows you to measure contribution margins per product, channel or campaign—and detect unprofitable listings early.

Returns and refunds also belong in the same lifecycle: the original sale is reversed, fees partially withdrawn, VAT adjusted, and the payout reconciled. Only then does your invoice management remain consistent and GoBD‑compliant.

3) VAT & OSS: clarity on countries, baskets and timing

In 2025, the OSS reporting logic remains central: key parameters are destination country, origin, tax rate and time of supply. Multi‑country setups (DE warehouse, EU fulfillment, possibly UK/US) increase complexity but are manageable if your transaction data is complete. It’s crucial that you interpret tax‑relevant fields from marketplace exports correctly (which is difficult to achieve manually) instead of relying on bank data alone. Only then will VAT returns, OSS and EC sales lists reconcile—and your reports withstand audits.

4) E‑invoicing & GoBD: manage invoices digitally, not as PDFs

With the B2B e‑invoicing obligation (phased start in 2025), a simple PDF no longer qualifies. XRechnung or ZUGFeRD provide structured data that accounting tools can process automatically. For online sellers, this means: create, receive, validate and archive invoices—immutable, traceable, and machine‑readable. The real question is not “How do I generate them?” but “How do I centrally manage invoices from Amazon, ERP and Shopify in a GoBD‑compliant way?”

5) Automation: from CSV to finished bookings

The path in 2025 is automated accounting. Systems fetch marketplace and PSP data, classify orders and fees, match payouts, create journal entries, and produce exports such as DATEV, Stotax, Lexware, SAP. This reduces errors, saves time, and ensures your financial data is tax‑ready daily, not just monthly. For scaling sellers, that’s the difference between “more sales” and more profit.

6) What KudTax does for you

KudTax is your central invoice and transaction management for e‑commerce. We generate e‑invoices and integrate with existing payment systems, ERP software and marketplaces. Our focus is data quality, automation and compliance:

KudTax automatically matches Amazon, Shopify and other marketplace transactions, links invoices, prepares data GoBD‑compliantly, and exports to systems like DATEV. You get clear management‑accounting figures, see where fees and returns erode margins, and steer your business with data instead of spreadsheets.

Additionally, KudTax, in collaboration with KudAccounting, offers to take over your complete ongoing bookkeeping.

7) Conclusion

Accounting for Amazon FBA and multi‑marketplace sales in 2025 is no longer document sorting—it’s data and process management. Those who model transactions granularly, handle e‑invoicing professionally and manage OSS correctly gain clarity and remain compliant. With KudTax, you build a scalable, automated accounting system—for less effort, more transparency, and a significantly better profit margin.