Connect Shopify with Fortnox in minutes

Connecting Shopify to Fortnox via Junipeer takes about 15 minutes for the technical setup. The time that varies is the configuration — mapping your sales accounts, VAT codes, and payment methods to Fortnox’s structure.

This guide covers what you need to prepare, how the connection works, and what to configure after connecting.

Before you start

Before connecting Shopify and Fortnox, make sure the following are in place in Fortnox:

1. An integration user with licences for Orders, Invoices, Accounting, and Integration. Do not use a personal account — create a dedicated user and do not modify it after the integration is live.
2. VAT rates configured for all your sales markets.
3. Sales accounts set up for each VAT rate and, if you sell to EU customers under OSS, for each EU country.
4. Payment method accounts mapped for each payment provider (Shopify Payments, Klarna, Stripe, Adyen, etc.). These map to a transit account — typically in the 19xx range — not directly to your bank.
5. Refund SKUs created: refund_discrepancy and refund_fee article numbers in Fortnox, needed to create credit notes.

See the Fortnox pre-integration settings guide for the full checklist.

What gets synced

Once connected, Junipeer handles the following flows between Shopify and Fortnox:

Shopify → Fortnox:

• Every order creates an invoice in Fortnox with the correct sales account, VAT code, and payment method
• Refunds create credit notes linked to the original invoice
• Klarna, Stripe, Adyen, and Shopify Payments payouts are reconciled against invoices automatically

Fortnox → Shopify:

• Stock levels update in near real-time to prevent overselling
• Product data and prices can flow from Fortnox to Shopify

OSS and EU VAT

If you sell to customers across the EU under One Stop Shop (OSS), each country requires its own sales account and VAT rate in Fortnox. Junipeer maps each order to the correct account based on the customer’s country. Configure this mapping during setup.

How to connect

1. In Junipeer, go to Connectors and add Shopify — you’ll be prompted to authorise via Shopify’s OAuth flow
2. Add Fortnox — enter the integration user credentials you created
3. Select the flows you want to activate (orders, stock, payouts, products)
4. Map your sales accounts, VAT codes, and payment methods
5. Run a test sync on a real order
6. Go live

For most single-store setups, this can be completed in a single session.