Domestic and foreign businesses registered for value added tax (VAT) in Estonia are typically required to submit monthly VAT returns through the Estonian Tax and Customs Board’s e-Tax/e-Customs portal (e-MTA).

Businesses with a turnover below €100,000 in the previous calendar year may request approval from the tax authority to file quarterly VAT returns, although this is subject to review and not guaranteed.

EU businesses do not need a fiscal representative to file VAT returns in Estonia. Non-EU businesses are generally required to file via a fiscal representative who is jointly liable for VAT obligations. However, in some cases — such as for certain electronically supplied services — a non-EU business may register and file directly without appointing a representative, if permitted by mutual recognition agreements or exemptions.

VAT returns must be filed online.

Businesses must report the following information when completing a VAT return in Estonia:

• Total taxable sales in Estonia

• VAT-exempt sales

• Intra-EU acquisitions and supplies

• Imports and exports

• Reverse charge transactions

• Amount of VAT collected (output VAT)

• Amount of VAT deductible (input VAT) 

• Net VAT payable or refundable

Registered businesses in Estonia can deduct VAT on goods and services used for taxable business activities, including:

• Goods purchased for resale

• Import VAT paid on goods brought into Estonia

• Business-related operational costs and capital expenditure

VAT is not deductible on:

• Personal employee expenses

• Certain entertainment or non-business-related costs

All VAT returns must be submitted by the 20th of the month following the end of the tax period. VAT due must also be paid by this deadline. Failure to file or pay on time may result in penalties and interest.

Late submission or payment results in interest of 0.06% per day on unpaid VAT.

Repeated non-compliance or negligence may lead to additional fines, which can reach up to €32,000 depending on the nature of the infraction.

If input VAT exceeds output VAT for a tax period, the resulting credit may be:

• Carried forward to offset future VAT liabilities; or

• Refunded directly — typically within 30 days if all filings are complete and documentation is provided

   

Refunds are subject to audit or review. Businesses should retain invoices and supporting records to justify VAT recovery claims.