Your Estonian OÜ needs its own accountant for its Amazon business — Amazon does not do that job for you. The marketplace becomes the deemed VAT supplier only when the underlying seller is established outside the EU; an Estonian company is EU-established, so the 24% VAT, the quarterly OSS return and the monthly reconciliation stay with you, not with Amazon’s tax engine. That single fact flips most of what is published on “Amazon accounting” online, because the majority of it is written for Chinese, UK or US sellers whose marketplace genuinely does collect VAT on their behalf. For an Estonian OÜ, your accountant instead needs monthly settlement reports, not just bank credits, and if you hold FBA stock in an EU warehouse you should expect a local VAT registration on top of OSS — plus a narrower choice of accounting providers, since some well-known names, Xolo among them, explicitly exclude e-commerce clients.
The short answer
An Estonian OÜ is EU-established, so Amazon is not the deemed supplier for your sales — the VAT obligation, at 24%, stays with you and your accountant, not with Amazon.
The EU-wide OSS distance-selling threshold is €10,000: below it you may charge your home Estonian rate, above it you charge the customer’s country rate, filed quarterly.
Your accountant needs Amazon’s monthly settlement/payout reports, not bank credits alone — one payout nets sales, refunds, commissions, FBA fees and ad spend into a figure that reconciles to nothing by itself.
Stock held in an EU fulfilment warehouse (classic FBA in Germany, Poland, Czechia) can trigger a local VAT registration in that country — OSS does not remove that obligation.
Goods already sitting in an EU warehouse fall outside the ≤€150 import simplification — that rule covers goods imported from outside the EU, not FBA stock already inside it.
Xolo, one of the best-known Estonian accounting providers, explicitly excludes e-commerce clients — confirm who actually covers marketplace accounting before you sign up.
Verified: August 2026
Who actually does the books for an Amazon seller’s Estonian OÜ?
Your own accountant does — the same one who files your Estonian KMD and annual report, not a service bundled into your Amazon seller account. That surprises founders who came from non-EU marketplaces, or who read US- and UK-focused guides where Amazon genuinely does collect and remit VAT on the seller’s behalf. An Estonian OÜ is an EU-established company, and the rule that hands VAT accounting to the marketplace only applies to sellers established outside the EU. Once you incorporate in Estonia, you have opted into being the party responsible for getting VAT right, which means you need someone who can read a settlement report as fluently as a bank statement.
Why doesn’t Amazon collect VAT for an Estonian company automatically?
Because the deemed-supplier rule that makes a marketplace responsible for VAT applies specifically when the underlying seller is not established in the EU — it was built to catch VAT on goods coming from outside the bloc, mainly from Chinese and other non-EU sellers, regardless of the value of the sale. An Estonian OÜ does not meet that condition, so Amazon has no legal basis to step into your shoes for VAT purposes. The practical effect: you register, you file, you remit — Amazon just pays out net proceeds and lets you sort the tax on the gross figure behind them. Every euro of VAT due on your EU sales is your company’s liability, reported on your own KMD and OSS returns, not absorbed anywhere inside Amazon’s systems.
What does your accountant actually need from you every month?
Settlement reports, not bank credits — that is the single most important habit to build. A single Amazon payout nets sales, refunds, commissions, FBA fees and advertising spend into one bank line, so the deposit hitting your account tells your accountant almost nothing on its own. Send the underlying report instead, plus the supporting data around it, every month without being asked. This is the same discipline any well-run Estonian company follows — see the general monthly checklist your accountant needs — just with e-commerce-specific inputs layered on top.
Amazon’s monthly settlement or payout report, showing gross sales, fees and refunds separately, not just the net transfer.
A per-country sales split, so OSS-eligible sales and domestic Estonian sales are never lumped together.
Refunds and chargebacks for the same period, matched to the original sale rather than netted informally.
Payment-provider reports — Stripe, PayPal or similar — where you take orders outside Amazon’s own checkout.
Stock movement records between warehouse countries, since a transfer between fulfilment centres is a reportable event, not just logistics.
Does OSS cover all my Amazon VAT?
No — OSS covers cross-border B2C distance sales within the EU, above the €10,000 EU-wide threshold, and nothing else. Below that threshold you may charge your home Estonian rate on those sales; above it, you charge the customer’s country rate and report it through OSS instead of registering in every destination country. What OSS does not cover: your domestic Estonian sales, which stay on the ordinary KMD, and any B2B sales, which follow their own rules. The OSS return is quarterly and separate from the monthly KMD — two returns, two rhythms, and mixing them up is the most common practical mistake founders make in their first year of Amazon selling. For the registration steps themselves, see the OSS registration walkthrough for Estonian e-commerce.
Scheme | What it covers | Return frequency |
|---|---|---|
OSS | B2C sales within the EU across borders, above the €10,000 EU-wide threshold | Quarterly |
IOSS | Goods imported into the EU, consignments valued at €150 or less | Monthly |
Neither (regular VAT) | Domestic Estonian sales, B2B sales, and sales from stock already held in an EU warehouse | Monthly KMD, by the 20th |
Does the €150 import simplification help with my FBA stock?
No — that simplification only applies to goods imported from outside the EU, and FBA stock already sitting in an EU fulfilment centre does not qualify. Goods already stored in an EU warehouse are not distance sales of imported goods, so they sit outside the imported-goods deemed-supplier framework entirely. In practice this means a unit you shipped once from outside the EU into, say, a German warehouse is now just ordinary EU stock: it is sold under the normal VAT rules for supplies made from that country, not under any import simplification, no matter how small the sale value is. Confusing the two is one of the most common — and most expensive — mistakes in Amazon-seller bookkeeping.
Does holding stock in a fulfilment centre create new VAT registrations?
Often, yes — storing stock in another EU member state (classic FBA fan-out across Germany, Poland or Czechia) means goods are being supplied from that country, and that is what triggers a local VAT registration obligation there. This is the part OSS does not fix: OSS does not remove a registration obligation created by holding stock in a country — it only simplifies the VAT on cross-border sales you make from your home country. We are deliberately not printing a table of country-by-country thresholds here, because the rules differ by member state and change without much notice; the honest answer is to check the specific requirement for each warehouse country with your accountant before Amazon routes stock there, not after.
The marketplace is the deemed supplier only when the seller is not established in the EU. An Estonian OÜ is EU-established — so Amazon does not account for your VAT, and the obligation stays with you.
Which Estonian accounting provider actually handles Amazon and e-commerce?
Not every Estonian accounting provider does — check before you commit, because settlement-report reconciliation is a genuinely different skill from invoicing a handful of B2B clients. Xolo explicitly excludes e-commerce from what it will take on, which removes one of the market’s best-known providers from consideration the moment your business model is FBA or marketplace sales. Look instead for a provider that names multi-country VAT, OSS and marketplace reconciliation as something they actually do, not just accounting in general terms — and ask, before signing anything, whether they have handled a settlement-report workflow before. If cost is part of your decision, see what accounting actually costs in Estonia as a starting benchmark, then ask specifically about e-commerce pricing, since it is rarely the same as the base tier.
What about banking for an Amazon-funded Estonian company?
Expect an EMI-first reality, the same as for any Estonian OÜ, because traditional Estonian banks often decline pure non-residents and push founders toward a payment institution instead. The account itself needs to produce a statement export your accountant can actually reconcile — a clean CSV or ISO 20022 feed, or a working integration — and support multiple currencies if you sell outside the euro area, which almost every Amazon seller does. Fintech prohibited-industry lists are long and routinely include categories close to e-commerce, so read the fine print before you apply rather than after a refusal. For a practical comparison of the options, see Stripe, Wise, Payoneer or a local bank for an Estonian OÜ.
Do you need an EORI number to sell on Amazon from Estonia?
Only if your goods physically cross the EU customs border — a pure intra-EU FBA setup, where stock only ever moves between EU warehouses, does not by itself require one. You need an EORI number the moment you import inventory from outside the EU, or export orders to non-EU customers such as the US, UK or Switzerland. It is issued free of charge by the Estonian Tax and Customs Board through the e-MTA portal, typically within 1–3 business days, and once issued it is valid across the whole EU, not just Estonia. A pure services business never needs one; a goods business that only ever restocks and sells inside the EU often does not either — it is specifically the crossing of the EU’s external border that triggers the requirement.
Do you need to file Intrastat for moving FBA stock between warehouses?
Only once your dispatches from Estonia exceed the 2026 threshold of €325,000 — below that, there is nothing to file. Intrastat is the statistical survey of intra-EU goods movements, filed monthly with Statistics Estonia, not EMTA, by the 14th of the following month; arrivals reporting was abolished in 2025, so only the dispatch side matters now. It does not apply to non-EU trade at all — a shipment to the US, UK or anywhere outside the EU is an export, handled through the customs declaration instead, never through Intrastat. Most founders in their first year or two of Amazon selling stay under the threshold and can ignore this entirely; it becomes relevant once FBA volume across several EU warehouses genuinely scales up.
What changes if you also ship orders into the US?
Expect every shipment to need a customs entry, because the old $800 de minimis exemption ended on 29 August 2025 for all countries, closing the low-value gap that used to let small parcels move without a formal entry. A temporary flat per-package postal duty, roughly $80–$200, ran only until 28 February 2026, and a new postal entry process for shipments up to $800 was being phased in through 2026 — treat the current mechanics as moving and check the process with US Customs and Border Protection directly rather than trusting an older guide. None of this changes your Estonian VAT position; it is a separate, US-side compliance layer that your accountant should know exists even though a customs broker, not your bookkeeper, usually files the actual entry.
What happens if you just let bank credits stand in for real accounting?
You lose the ability to prove your VAT figures, and that is exactly what an audit tests first. Consider a founder who reconciles only the net Amazon payout each month: refunds get buried inside a lower deposit, FBA fees never show up as a deductible cost on their own line, and the per-country sales split needed for OSS simply does not exist anywhere in the books. When EMTA or a bank asks for the underlying detail, “it matches what Amazon paid us” is not an answer — the settlement report is the primary record, and the bank line is only ever a summary of it. Rebuilding that detail after the fact, quarter by quarter, costs far more accountant time than sending the reports monthly from the start.
A practical monthly workflow for Amazon accounting
Treat this as a checklist you run every single month, not something you reconstruct at year-end. The order matters: settlement data first, country splits second, everything else layered on top, because getting the first two steps wrong propagates errors through the rest of the file.
Export the Amazon settlement/payout report for the closed period as soon as it is available.
Split sales by country and flag which are OSS-eligible versus domestic Estonian sales.
Log refunds and chargebacks against the original sale, not as a standalone adjustment.
Pull payment-provider reports (Stripe, PayPal, Payoneer) for any orders taken outside Amazon.
Record stock movements between warehouse countries, including any new country a shipment reached for the first time.
File the KMD by the 20th every month, and the OSS return in the relevant quarter’s deadline.
Flag any new warehouse country to your accountant immediately — it may mean a fresh local VAT registration before OSS can help.
Frequently asked questions
Does Amazon pay VAT on my behalf if I run an Estonian OÜ?
No. Amazon only becomes the deemed VAT supplier for sellers established outside the EU. An Estonian OÜ is EU-established, so the VAT obligation on your sales stays with your company, not with Amazon.
What VAT rate applies to my Amazon sales as an Estonian company?
Estonia’s standard VAT rate is 24%. Domestic Estonian sales and sales below the €10,000 OSS threshold use that rate; above the threshold, cross-border EU B2C sales use the customer’s country rate, reported through OSS.
Do I need to register for VAT in every country where my FBA stock is stored?
Possibly — storing stock in another EU country creates a local registration obligation there, because the goods are supplied from that country. We do not publish per-country thresholds here since they differ and change; check the specific rule for each warehouse country with your accountant.
Does OSS remove the need for a local VAT registration where I hold stock?
No. OSS simplifies VAT on cross-border sales made from your home country, but it does not remove a registration obligation that storing stock in another country creates.
Is FBA stock covered by the €150 import VAT simplification?
No. That simplification applies only to goods imported into the EU from outside it. Stock already sitting in an EU warehouse is not an import and follows the normal VAT rules for supplies made from that country.
What documents does my accountant need each month for an Amazon business?
Amazon’s settlement or payout report, a per-country sales split, refunds and chargebacks for the period, payment-provider reports for any non-Amazon checkout, and records of stock movements between warehouse countries.
Can I use Xolo for Amazon or e-commerce accounting?
No. Xolo explicitly excludes e-commerce clients, so an Amazon seller needs a different Estonian accounting provider, ideally one that names marketplace and multi-country VAT reconciliation as work it actually does.
Do I need an EORI number to sell on Amazon from Estonia?
Only if goods physically cross the EU customs border — importing stock from outside the EU or exporting orders to non-EU customers. Pure intra-EU FBA movement between warehouses does not, by itself, require one.
Do I need to file Intrastat for moving FBA stock between EU warehouses?
Only once your dispatches from Estonia exceed the 2026 threshold of €325,000. Below that, and for any non-EU trade, there is nothing to file under Intrastat.
