Record Shopify sales in Fortnox

Connecting Shopify to Fortnox means your sales are automatically recorded as invoices — but there are specific things you need to understand about how Shopify structures its financial data and how that maps to Fortnox accounts.

This guide covers the key accounting concepts: how orders, fees, and payouts flow from Shopify into Fortnox, and what you need to configure.

How Shopify orders flow into Fortnox

When a customer places an order in Shopify, that order needs to become an invoice in Fortnox with:

• The correct sales account (typically 3001 for goods at 25% VAT, 3002 for 12%)
• The correct VAT code based on the customer’s country and product type
• The payment method mapped to a transit account (not your bank account directly)

With Junipeer, each order is mapped automatically based on the rules you configure during setup.

How Shopify fees are recorded

Shopify deducts its transaction fee from the payout before sending money to your bank. This means:

• The payout amount is less than the sum of orders
• The fee difference needs to be recorded as an expense in Fortnox (typically account 6570 or 6590)

With Junipeer, the fee is automatically split from the payout and booked as a separate expense line.

Payout reconciliation

Shopify Payments (and Klarna, Stripe, Adyen) send aggregated payouts — a single transfer that covers many orders. Reconciling these manually against individual invoices is time-consuming. Junipeer matches each payout to the corresponding invoices automatically.

OSS VAT for EU sales

If you sell to customers in EU countries, you need a separate sales account and VAT rate per country in Fortnox. Junipeer maps each Shopify order to the correct account based on the customer’s shipping address and the OSS rules you’ve configured.

Refunds and credit notes

Refunds in Shopify create credit notes in Fortnox, linked to the original invoice. This maintains the correct audit trail and inventory records. The refund_discrepancy and refund_fee article numbers in Fortnox are required for this to work.

What you need to set up in Fortnox first

Before going live:

• Sales accounts for each VAT rate (and per EU country for OSS)
• Payment method accounts (19xx-series) for each payment provider
• refund_discrepancy and refund_fee article numbers
• A dedicated integration user with correct licence permissions

See the Fortnox pre-integration checklist for the complete list.