Shopify + Fortnox: How Bookkeeping Works

Updated March 22, 2026

Understanding the bookkeeping flow

When an order is placed in Shopify and captured, Junipeer creates:
- An Order in Fortnox
- An Invoice when payment is captured
- The invoice is set to the payment method configured in your mapping

Refund Flow When a refund occurs in Shopify: - A Credit Invoice is created in Fortnox - It is linked to the original invoice - Important: Only 1 credit invoice per invoice is supported by Fortnox

Payment Reconciliation When the payment provider (Shopify Payments, Klarna, Adyen, Svea, etc.) issues a payout: - Each payout line is matched to the corresponding invoice - Provider fees are posted as write-offs - The payout is booked to your configured payout account (typically 19xx series)

OSS (EU One-Stop-Shop) For cross-border B2C sales within the EU, Junipeer maps sales to per-country accounts using 3000-series sales accounts. Configure this in the Sales Account Mapping settings.

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