E-commerce and VAT for Estonian companies

What Estonia expects of an online seller

An Estonian company that sells online has VAT duties in Estonia. The standard rate has been 24% since 1 July 2025, and the registration threshold is 40,000 EUR. We check with you whether registration is needed and from when, and we handle it. The Estonian VAT guide for 2026 has more detail.

The monthly KMD cycle

Once the company is registered, we file the VAT return (KMD) every month, by the 20th of the following month. In plain terms, you tell the Tax Board each month how much VAT you charged and paid, and settle the difference. The steps are these:

1. We receive the month's sales, refunds and expenses.
2. We record sales by country of delivery and deal with the VAT on each.
3. We prepare the KMD for the management board to approve.
4. We file the return by the 20th and close the month.

OSS and IOSS on the Estonian side

Where your sales make OSS or IOSS relevant, those returns are part of our Estonian work. OSS (One Stop Shop) and IOSS (Import One Stop Shop) are EU schemes. They let a seller report, in one country, the VAT on certain sales to consumers in other EU countries. At the start we confirm with you whether they apply to your business, and we add them to the monthly calendar. Our page on e-commerce accounting with OSS and IOSS has the detail.

What the books need every month

An online shop produces many small transactions. For the books to close without gaps, each month we need:

• the sales report from each shop or platform, with the country of delivery of every order,
• payment provider reports, with gross amounts, fees and payouts,
• refunds and returns,
• bank statements of the Estonian company,
• purchase, shipping and advertising invoices,
• a stock record or, at least, the cost of goods sold.

Without this, we cannot close the month's VAT. If months are missing, catch-up bookkeeping fills them in before new returns are filed.

If you sell to customers in several countries, record the country of delivery for each sale, because the VAT treatment can depend on it. That is why we ask for sales reports that include that field, not just totals.

Where an online shop's books usually go wrong

• Bundled payouts: the platform transfers one net amount for many orders. Without the payment report, the bank cannot be matched to the sales.
• Fees and refunds posted from the bank statement alone, with no report behind them.
• Sales with no country of delivery, so the VAT on each one cannot be worked out properly.
• Months in which nobody closed the stock, so the cost of goods sold is only an estimate.

At the start we agree how each source reaches us and who sends it. That way the monthly close does not depend on anyone remembering.

Where Estonia ends and Portugal begins

We do not state Portuguese VAT rates or thresholds. These are questions for your adviser in Portugal:

• What VAT obligations arise in Portugal when you deliver to Portuguese customers?
• How do those obligations fit with the Estonian registration and with OSS?
• What sales information does your contabilista certificado need each month?

Residence matters for online shops too

An online shop run from Portugal raises the same question as any company. Article 2(3) CIRC, the Portuguese corporate income tax code, treats an entity with its sede (registered seat) or direção efetiva (place of effective management) in Portugal as resident there. The Estonian register does not settle this on its own. Our page on an Estonian company with a Portugal-resident owner explains the point, and the answer belongs with your contabilista certificado.

What we do

We do the monthly bookkeeping, the Estonian VAT registration and returns, OSS and IOSS where they apply, and the annual report. If an Estonian company does not help your business, we will say so.

We prepare the returns, and the Estonian management board approves and signs them. Your contabilista certificado receives the Estonian figures in a form ready to consolidate and keeps handling everything Portuguese.