Fortnox is the dominant ERP system for Swedish ecommerce businesses. This guide explains what happens when you connect Fortnox to an ecommerce platform like Shopify or WooCommerce via Junipeer — what data flows, what you need to set up in Fortnox beforehand, and what to watch out for.
What gets synced between Fortnox and ecommerce
From ecommerce to 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
From Fortnox to ecommerce:
- Stock levels update in near real-time to prevent overselling
- Product data and prices can flow from Fortnox to the webshop
Before you start: Fortnox configuration
Before connecting, make sure Fortnox has:
- A dedicated integration user with licences for Orders, Invoices, Accounting, and Integration
- VAT rates configured for all sales markets (including EU countries if you sell under OSS)
- Sales accounts mapped per VAT rate and per EU country for OSS
- Payment method accounts for each payment provider (typically 19xx-series transit accounts)
- Refund SKUs:
refund_discrepancyandrefund_feearticle numbers in Fortnox
See the full pre-integration checklist for details.
OSS and EU VAT in Fortnox
If you sell to EU customers under One Stop Shop (OSS), each country requires its own sales account and VAT code in Fortnox. The integration maps each order to the correct account based on the customer’s country. You configure this mapping once during setup — after that it runs automatically.
How the connection works
- Connect Fortnox in Junipeer using your integration user credentials
- Select which flows to activate (orders, stock, payouts, articles)
- Map sales accounts, VAT codes, and payment methods
- Run a test sync on a real order
- Go live
The technical connection takes about 15 minutes. Configuration time varies with the complexity of your account structure.