Accounting & Tax for E-commerce Businesses in Estonia

No — that is exactly what the OSS scheme prevents. If your total B2C cross-border sales to other EU countries exceed €10,000 per year, you register for OSS through the EMTA e-Tax portal (one registration, in Estonia). You then charge each country’s correct VAT rate, file a single quarterly OSS return covering all EU countries, and pay the total to EMTA in one transfer. EMTA distributes the amounts to each member state. The only exception is if you hold stock in another EU country (e.g. via Amazon FBA warehouses) — stock-holding countries require local VAT registration separately from OSS.

Stripe processing fees are recorded as cost of revenue (COGS) — they are a direct cost of generating each sale. The correct accounting entry is: DR Revenue (gross sale amount), CR VAT Liability (VAT collected), CR Stripe Fee Expense (processing fee), CR Cash/Bank (net settlement received). Shopify’s monthly subscription fee is a general operating expense (not COGS) — it is a platform cost not tied to individual transactions. Both are deductible business expenses for the OÜ. On your management accounts, they should appear on separate lines so you can track payment processing costs as a percentage of revenue over time.

A refund requires a credit note referencing the original invoice. The credit note reduces your revenue, your VAT liability, and — if the goods are returned in saleable condition — restores the inventory. The VAT adjustment is made in the month the credit note is issued, not in the month of the original sale. On the KMD return for the month you issue the credit note, your output VAT is reduced by the VAT content of the refund. If the refund crosses a VAT period boundary (original sale in Q1, refund in Q2), the KMD adjustment goes in Q2. Keep both the original invoice and the credit note on file — EMTA may request evidence of the transaction chain.

Storing goods in Germany — even through Amazon FBA — creates a VAT presence in Germany that requires German VAT registration. This is separate from OSS and from your Estonian VAT registration. You must register for a German Umsatzsteuer number (typically via a local German tax adviser or through Amazon’s VAT Services), file monthly/quarterly German VAT returns, and account for German VAT on domestic German sales (sales where both buyer and stock are in Germany). This also creates potential German trade tax (Gewerbesteuer) exposure — a permanent establishment analysis is recommended. The same logic applies to France, Poland, or any other EU country where Amazon FBA holds your inventory.

USD payments from US customers must be converted to EUR for your accounts. The exchange rate to use is the rate on the date of actual receipt into your account (not the invoice date). Under Estonian and IFRS rules, monetary items (bank balances in USD) must be restated at the month-end rate, with FX gains or losses posted to P&L. In practice: record the USD receipt at the day’s rate in your accounting software, maintain a separate USD account in your chart of accounts, and run FX revaluation at month-end. For US customers, EU VAT generally does not apply (supplies outside EU VAT scope), but US sales tax rules may create obligations depending on your nexus — this is covered in detail in the cross-border taxation section.