You can run a German FBA business for months on a profit number that looks right and is quietly wrong. German VAT touches your margin in three separate places, and only one of them looks like tax.
Here are the three, in the order they bite.
1. Import VAT is a cash-flow event, not a cost
When your goods enter Germany from outside the EU, import VAT (Einfuhrumsatzsteuer) is charged, usually at 19 percent, on the customs value plus duty and shipping into Germany. If you are registered for German VAT, the goods are for your business and the import runs in your company’s name, you get it back: it goes into your VAT return as input tax and is set against what you owe.
The catch is timing. Germany has no postponed import VAT accounting of the kind the Netherlands operates, where the import VAT and its deduction cancel out on the same return and no money moves. In Germany the money genuinely leaves at the border, in practice often fronted by your freight forwarder and invoiced straight back to you, and comes back later through the return. A deferment account (Aufschubkonto) shifts the payment date, but it does not remove the payment.
On a first shipment worth 50,000 euros that is roughly 9,500 euros gone before you have sold a single unit, returning weeks later.
There is a second timing risk on top of the payment itself, and it sits before the money even starts moving back. To deduct the import VAT on your return, you need the right customs document in hand, not just proof that you paid. German law requires the Einfuhrabgabenbescheid (the customs assessment notice issued after your import declaration is processed), or a certified substitute document confirmed by the customs office. Where the import runs through the ATLAS electronic procedure, an electronic printout of the transmitted assessment is accepted instead. Without one of these, the deduction is not possible, no matter how clearly the payment shows up on your bank statement.
In practice this document is usually issued to your freight forwarder or customs agent, not to you directly, and it needs to be in your company’s name to count as your proof. If the forwarder is slow to pass it on, or acted in “indirect representation” (in which case they become a co-debtor for the import VAT themselves), getting the paperwork together can lag behind the actual cash outflow by weeks, which pushes your recovery into a later VAT return than the shipment itself would suggest. Build that document lag into your cash plan alongside the return cycle itself.
Two documents are worth filing systematically for every shipment: the Einfuhrabgabenbescheid itself, which is the primary and, in practice, indispensable proof, and the separate payment or settlement receipt from your forwarder or customs showing the import VAT was actually paid. Keep both for ten years, the retention clock German law puts on customs documentation. They do not normally need to be submitted upfront, but they are what you will be asked to produce if a return is ever queried.
Two ways this distorts a P&L. Book it as a cost and your landed cost per unit is inflated, so your margin looks worse than it is and you may price too high. Forget it entirely and your cash forecast is wrong in the one month you can least afford it, which is the month you are also paying for stock and freight.
It is neither. It is working capital, and it belongs in your cash plan rather than your cost of goods.
2. Whether you collect the 19 percent depends on where your company is, not where your stock is
This is the one that surprises people, and it splits Amazon sellers into two groups that see completely different numbers for identical businesses.
If your company is established outside the EU, and Amazon ships to a German consumer from a German warehouse, German law treats Amazon as the supplier for that sale. Amazon charges the VAT and pays it to the tax office. You never touch it. Your settlement will not show German VAT flowing through your account, because it did not. One boundary to keep in view: this covers sales to consumers. A business customer ordering through the platform is buying from you under the ordinary rules, and that invoice is yours.
If your company is established inside the EU, the ordinary rules apply. You charge the 19 percent, it lands in your account, and you pay it over. It appears in your revenue line and it was never yours.
Same product, same warehouse, same German customer, same platform. The tax treatment differs entirely because of where the selling company sits. If you have ever compared numbers with another seller and found their VAT position made no sense next to yours, this is usually why.
Now the part that costs people money. Being in the first group does not mean you have no German VAT obligation. Your stock sitting in a German warehouse is still a taxable presence. You still register, you still file returns, you still report those supplies, and you still need the registration to recover the import VAT from point 1. Sellers who conclude “Amazon handles my VAT, so I have nothing to do in Germany” are the ones we later meet holding a stack of overdue returns, and the German late-filing surcharge has no percentage cap. It is 0.25 percent of the assessed tax per started month of delay, with a minimum of 25 euros per month, per return.
3. Your payout is not your revenue, and neither is your taxable base
Three different numbers describe the same month, and a profit calculation that treats any two of them as interchangeable will drift.
The payout that reaches your bank is net of Amazon’s fees, refunds and adjustments. The revenue you report is gross of those fees. The taxable base for VAT follows its own rules again: refunds reduce it, but in the period the refund happens rather than the period of the original sale, so a heavy returns month pulls your VAT down after your revenue has already been counted.
Amazon’s fees add one more wrinkle. They are usually invoiced to a VAT-registered seller without VAT, and you account for the tax on them yourself under the reverse charge. You declare it and, in the same return, deduct it, so the net effect is normally zero. It still has to appear on the return. The number is not optional just because it cancels out.
A month makes it concrete. Say you are an EU-established seller and German consumers paid you 50,000 euros in total, Amazon’s fees for the month were 8,000 euros, and 3,000 euros of goods came back.
Your payout is roughly 39,000 euros. Your revenue is 42,017 euros, because the 50,000 your customers paid contains 7,983 euros of VAT that was never yours. Your VAT base starts from that same 42,017, but the returned goods come out of it in the month the refunds are paid, not the month of the original sales, and only at their net value of roughly 2,500 euros. The 8,000 in fees appears on your return twice, declared and deducted, netting to nothing while still being reportable. And the 39,000 that did reach your bank is not all yours either: roughly 7,500 euros of it is VAT on the sales that stuck, waiting for the return that hands it over.
Four numbers, one month, one bank transfer, and no two of them agree.
All three are ordinary numbers doing their ordinary jobs. The gap between them is where a profit tool and a tax return stop agreeing.
What this means for your numbers
Four habits keep the picture honest.
Treat import VAT as working capital. Give it its own line in the cash plan, and keep it out of cost of goods, so your unit economics are not permanently distorted by money you will get back.
Know which side of the deemed-supplier rule you are on. It is determined by where your company is established, not where your stock is, and it changes what you should expect to see in a settlement report. If you are not certain, that is worth ten minutes with an advisor rather than an assumption.
Reconcile to gross, not to payout. Your VAT return is built from what your customers paid, not from what Amazon transferred to you.
Do not read Amazon collecting the VAT as Amazon handling your compliance. It handles one specific sale in one specific direction. Your registration, your returns and your import VAT recovery all remain yours.
Get those four right and your margin number stops moving every time somebody looks at it more closely. German VAT rarely destroys a good business. What it does, quietly and repeatedly, is make a good business think it is doing better or worse than it is, for a year, until the first letter from the tax office arrives and the arithmetic has to agree.
Michael Stiller is a Steuerberater (German certified tax advisor) and Expert-Comptable, registered with the Steuerberaterkammer Rheinland-Pfalz. He and the team at Vaytax (vaytax.com) handle German VAT registration and filing for foreign online sellers.
