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Stripe payouts in e-conomic: sales, fees and refunds

How to book a Stripe payout: sales in the right VAT period, fees with the right VAT and a bank that matches to the øre.

Updated October 20, 2026

Stripe gathers sales, refunds, fees and disputes on a balance and pays it out to the bank a few days later. The bank line is therefore rarely one sale, and it often falls on another day, and sometimes in another VAT period, than the sale. This guide shows how to book Stripe payouts correctly in e-conomic, with sales, refunds, fees and VAT.

What a Stripe payout holds

In the Stripe Dashboard you find each payout under Balances → Payouts. A payout shows the transactions it is made of:

The "Payout reconciliation" report gives the same figures for a whole period.

The principle: Stripe receivable

Use a clearing account, a balance account such as "Stripe receivable", for the money Stripe holds for you. Sales go in on the day they hit the Stripe balance. Refunds and fees go out on the day they happened. The payout moves the rest to the bank on the day the money arrived. When a payout is done, the account stands at zero, and the bank line matches the payout exactly.

The dates matter. A sale on 30 June paid out on 2 July belongs to the second quarter. Book everything on the payout day, and the sales and VAT move into the wrong period.

Is the sale invoiced, or is the payout the sale?

Before you book, you must know where the sale is counted. It may be counted in one place only:

Example: the payout is the sale

Stripe pays out DKK 2,402.15 on 15 October for sales on 13 and 14 October of DKK 2,500.00 including VAT, a refund of DKK 50.00 and fees of DKK 47.85:

EntryDebitCreditAmount
Oct 13–14 salesStripe receivableSales (25% VAT)2,500.00
Oct 14 refundSales (25% VAT)Stripe receivable50.00
Oct 14 feesFeesStripe receivable47.85
Oct 15 payoutBankStripe receivable2,402.15

In: 2,500.00. Out: 50.00 + 47.85 + 2,402.15 = 2,500.00. Revenue is DKK 2,450.00 including VAT, not the DKK 2,402.15 that reached the bank. The difference is Stripe's fees, which are an expense.

Stripe's fees and VAT

Stripe charges two kinds of fees, and the VAT differs:

Keep the two on separate accounts, so the VAT can be set right. Stripe issues a monthly statement of its fees that your bookkeeper can use as a voucher. Ask your accountant which VAT code to use.

Disputes and currency

Common mistakes

Questions about Stripe in e-conomic

Why does the Stripe payout not match the day's sales?

Because Stripe pays out with a delay and gathers several days of sales, refunds and fees in one payout. Reconcile the payout against its own transactions in Stripe, not against the sales on the payout day.

Should Stripe subscriptions be booked differently?

If you use Stripe Billing and send Stripe's invoices to e-conomic, the sale is invoiced there. The payout must then not be booked as sales again; the payments should close the invoices or go to a balance account without VAT.

Automatically with 2app

2app reads each Stripe payout with a restricted key that may only read, and puts it in a daybook in e-conomic. Sales, refunds, disputes and fees are dated the day they hit the balance, and the payout the day the money reached the bank. Everything goes through Stripe receivable, which comes to zero. Stripe's own services can get their own account and VAT code. A payout that does not add up to the øre is stopped and shown, and you book the daybook yourselves. If the orders come from a webshop, they can become invoices with WooCommerce to e-conomic, and each Stripe payment then closes its invoice.

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