Shopify Payments for an Estonian Company: Setup, Payouts and Fees

Shopify Payments is Shopify’s built-in payment system. It accepts cards, Apple Pay and Google Pay without a separate payment provider and spares you the third-party transaction fee charged on orders paid through other providers. Shopify Payments became available in Estonia in March 2025, so older guides that call it unavailable there or tell you to connect Stripe for card payments are out of date.

Can an Estonian Company Use Shopify Payments?

Yes. Shopify’s requirements for Estonia state that a company’s representatives do not have to live in Estonia, as long as the company is registered in Estonia and has a registered address there. E-residents living abroad usually cover the address requirement with a registered address service.

Individuals and sole traders are the exception: they must live in Estonia or use a Shopify Payments account for the country where they live. A founder living abroad can therefore get an Estonian Shopify Payments account only through a company. Whatever the legal form, some business types cannot use Shopify Payments at all, so check Shopify’s list of prohibited businesses before you build the store.

How to Set Up Shopify Payments for Your OÜ

You can turn on Shopify Payments under Settings > Payments in the Shopify admin. The company must already be in the Commercial Register, so this step comes after company formation through e-Residency or through a notary.

1. Set Estonia as the store’s business country and choose Private corporation as the business type.
2. Enter the company’s name, registry code, registered address and VAT number (if it has one) exactly as they appear in the register, including letter case and punctuation.
3. Add everyone who holds 25% or more of the company as an Owner, exactly as the register shows them. These are usually the company’s beneficial owners.
4. Add the account representative (a beneficial owner or an executive with decision-making power) with their personal and contact details, job title and shareholding.
5. Link the company’s euro current account.

Verification Documents Shopify May Ask For

Shopify asks for documents only when it cannot confirm your details automatically. The usual set is a valid passport or ID card and a Commercial Register extract for the company, plus proof of the representative’s home address issued within the last six months, such as a utility bill or bank statement. Photograph paper documents with a camera, as Shopify rejects scans, photocopies and screenshots. Upload digitally issued documents as the original PDF with all pages.

In European countries, accounts opened from June 2026 have 90 days from the first processed order to complete verification, so start early. If verification is not finished in time, Shopify pauses payouts and then stops accepting Shopify Payments orders until it is complete. After the 90 days, it may refund orders.

Which Bank Account to Link for Shopify Payouts

The payout account must be a current account in euros that receives SEPA transfers. Shopify accepts IBANs from most EU countries as well as Norway, Switzerland, the UK and Gibraltar, so the bank does not have to be Estonian. It does not accept savings accounts, accounts that hold several currencies at once or services that only imitate a bank account.

Fintech accounts such as Wise Business or Revolut Business give a company a euro IBAN from an accepted country. Shopify accepts virtual accounts like these but warns that payouts to them fail more often, and their multi-currency setup may conflict with the rule above. A current account at a bank is therefore the most reliable choice, although banks are cautious with companies run from abroad, as our guide to bank accounts for non-resident companies explains.

Choose the account carefully, because each change puts payouts on hold for 3–5 business days and the hold cannot be lifted.

How Shopify Payouts Work

Shopify collects each payment, holds it for the settlement time and then sends the money to your bank as a payout. These are the main rules for Estonian stores, based on Shopify’s payout page for Estonia and its payout schedule settings:

New stores start with longer settlement times, which Shopify can shorten once you fulfil orders reliably and on time.

If a customer disputes a payment, Shopify immediately takes the disputed amount and a €15 chargeback fee from your balance and returns both if you win. Anything the balance cannot cover comes out of later payouts.

Euro payouts carry no extra fee. If you also sell in pounds or dollars, Shopify converts those payments to euros and charges a currency conversion fee. For stores outside the United States it is 2%, so take it into account before you switch on local currencies.

Shopify Payments Fees and the Third-Party Transaction Fee

Shopify Payments charges a processing fee on every card payment. The rate is lower on more expensive plans and varies by country, so check your store’s figures under Settings > Payments before you activate Shopify Payments.

Orders paid through another payment provider carry Shopify’s third-party transaction fee on top of that provider’s own fee:

On a €100 order paid through another provider on the Basic plan, Shopify keeps €2 before the provider charges anything. According to Shopify’s help page, orders paid through Shopify Payments or Shop Pay carry no such fee, and neither do manual methods such as bank transfer. PayPal orders are exempt too, as long as Shopify Payments is your primary payment provider. Any other provider you add alongside Shopify Payments still triggers the fee, and Shopify does not return it when you refund an order.

Bank Links and Local Payment Methods on Shopify

Shopify Payments accepts Visa, Mastercard, American Express and UnionPay cards, plus Apple Pay, Google Pay and Shop Pay. You can also switch on local payment methods that customers see in their own countries, such as BLIK in Poland, Bancontact in Belgium and MobilePay in Denmark and Finland. Klarna works for customers in many European countries, but not in the Baltic States. In Estonia, Shopify Payments covers online sales only, so selling in person through Shopify POS needs a card terminal from another provider.

Shopify Payments does not include bank links, the redirect to the customer’s internet bank that is a common way to pay online in Estonia, Latvia and Lithuania. If you sell in the Baltics, you can add them through a local provider’s Shopify app, such as Montonio, MakeCommerce (Maksekeskus) or OPAY. Each of these orders then costs the provider’s fee plus Shopify’s third-party transaction fee, so compare the total with card payments.

Shopify Payouts and Your Company’s Accounting

A Shopify payout is a net amount: sales minus Shopify’s fees, refunds and any chargebacks. Your accountant needs the payout reports from the Shopify admin to record each sale at its full value and the fees as expenses.

The money belongs to the company, so pay yourself from its account as a salary, board member fee or dividend. Our comparison of salary and dividends shows how each is taxed. If you sell to consumers in other EU countries, read our guide to VAT OSS for e-commerce.

How Eesti Firma Helps

We register Estonian companies for online businesses run from abroad, through e-Residency or by power of attorney through a notary, and provide the registered address in Estonia that Shopify requires. Our accounting team then keeps the books of online stores, including Shopify payouts, fees and OSS returns.

If you are planning a Shopify store under an Estonian company, send us a short description of your business and we will suggest how to set up the company and its accounting.

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