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Webshop bookkeeping in e-conomic: sales, payments and reconciliation

The orders are the sales, the payout is a payment: how to book a webshop in e-conomic with a clearing account that comes to zero, and reconcile every month.

Updated November 9, 2026

A webshop gives the books two streams to keep track of: the sales, meaning the orders, and the money, meaning the payouts from Shopify Payments, Stripe, MobilePay, Klarna or Nets. The two arrive on different days and with different amounts, which is why webshop bookkeeping so often ends in differences. This guide shows how to keep them apart in e-conomic, make them meet on a clearing account that comes to zero, and reconcile it all every month.

Two streams: the sales and the money

If you book the payout as revenue, revenue and VAT come out too low and the fees disappear. If you book both the orders and the payout as sales, the sales count twice. The rule is simple: the orders are the sales, and the payout is a payment.

The sales: pooled per day or one invoice per order

There are two ways to book the sales:

If you have more than a handful of orders a week or customers in other EU countries, one invoice per order is almost always right. How it is done on each platform is in the guides for Shopify, WooCommerce and Magento 2.

The money: one clearing account per payment provider

Create a balance sheet account in e-conomic for each payment provider, such as "Shopify Payments receivable" or "Stripe receivable". Everything that happens at the provider is booked through that account:

  1. The payments close the invoices: debit the clearing account, credit the debtor.
  2. Refunds go the other way: credit the clearing account, debit the debtor, against the credit note.
  3. The fees are booked on a fees account with the VAT the provider's fee invoice states, and credited to the clearing account.
  4. The payout to the bank is credited to the clearing account and debited to the bank.

When everything for a payout is booked, the clearing account stands at zero. If an amount is left, a payment, a refund or a fee is missing.

Example: one payout from Shopify Payments

The payout covers three orders totalling DKK 1,575.10, a refund of DKK 199.00 for an earlier order and fees of DKK 38.75. The bank receives DKK 1,337.35:

EntryClearingContra account
Payments for orders #1042, #1043 and #1044+1,575.10Debtors (closes the invoices)
Refund for order #1040−199.00Debtors (against the credit note)
Fees−38.75Fees
Payout to the bank−1,337.35Bank
Balance0.00

Revenue and VAT came with the invoices when the orders were placed. The payout does not change them; it only moves the money from the provider to the bank. The details for each provider are in the guides for Shopify Payments, Stripe and MobilePay.

VAT: Denmark, the EU and OSS

The VAT in the books must be the VAT the webshop actually charged the customer. So the webshop's tax settings must match your registration before it makes sense to look at e-conomic.

Reconciling every month

Common mistakes

Questions about webshop bookkeeping

Which date should the sale have?

The order date, or the date the goods were delivered if you invoice on shipping. Not the payout date: then a sale can land in the wrong VAT period when a payout crosses a month end.

Do fees from payment providers carry VAT?

It depends on the provider and where it is based. Book the fees with the VAT stated on the provider's fee invoice or report, and ask your accountant if the provider is abroad.

Can we just book the sales pooled per day?

Yes, if you sell little and only to Denmark. As long as there are few refunds and no OSS VAT, it can be enough. When sales grow, or customers in other EU countries arrive, one invoice per order is easier to keep track of.

Automatically with 2app

2app can do both streams automatically. Webshop apps such as Shopify to e-conomic, WooCommerce to e-conomic, Magento 2 to e-conomic and PrestaShop to e-conomic turn the orders into invoices in e-conomic. Payment apps such as Shopify Payments to e-conomic, Stripe to e-conomic and MobilePay to e-conomic put the payouts in a cash journal, where the payments close the invoices and the fees stand on their own. A payout that does not match to the øre is stopped and shown.

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