What the integration actually does
When you connect an ecommerce platform like Shopify, WooCommerce, or Magento to Fortnox through Junipeer, the integration handles four main data flows:
Orders and invoices. When a customer places an order in your store, Junipeer creates an order in Fortnox. When the order is captured (paid), an invoice is created automatically. The invoice includes line items, VAT, shipping costs, and customer information — mapped to the right accounts in Fortnox.
Credit invoices. When a refund is issued in the ecommerce platform, Junipeer creates a credit invoice in Fortnox linked to the original invoice. One important limitation: Fortnox only supports one credit invoice per invoice. If you need to issue a second refund on the same order, that needs to be handled manually in Fortnox.
Payouts. Payment provider settlements (from Shopify Payments, Klarna, Adyen, Stripe, and others) are matched to invoices in Fortnox and marked as paid. Provider fees are posted as write-offs. This gives you full reconciliation between what the payment provider settles and what Fortnox records.
Products and stock. Articles and stock levels can sync in both directions. Typically, stock levels flow from Fortnox to the ecommerce platform to prevent overselling, while new products created in the store flow back to Fortnox.
What you need to configure
The connection itself takes about 15 minutes. The configuration that matters is the data mapping:
Sales accounts. You need to decide which Fortnox accounts orders should post to. If you sell to multiple EU countries, you will need to set up OSS (One-Stop-Shop) mappings — one sales account per country, using 3000-series accounts (not 2000-series VAT accounts).
VAT handling. Fortnox includes 25%, 12%, and 6% VAT rates by default. If you sell to other EU countries, you need to add their VAT rates manually in Fortnox before the integration can use them.
Payment method mapping. Each payment gateway in your store (Klarna, Swish, card payments) maps to a payment method in Fortnox. Getting this right is important for reconciliation.
Shipping method mapping. Shipping methods from the ecommerce platform map to delivery methods in Fortnox.
Common things to watch out for
Date differences. Your ecommerce platform uses the order creation date. Fortnox uses the invoice/booking date. These can differ by days, which means monthly revenue reports may not match perfectly between the two systems. This is expected — compare using invoice dates in Fortnox.
Product number format. Fortnox product numbers only allow letters, numbers, and a few special characters (underscore, dash, forward slash, backslash, plus, dollar sign). No spaces. If your store uses SKUs with spaces or other characters, they will need to be cleaned up.
Invoice finality. Once an invoice is created and booked in Fortnox, it cannot be modified through the API. If an order needs to be corrected after invoicing, you need to create a credit invoice and re-invoice.
Warehouse module. If you use the Fortnox Warehouse Module and a product has zero stock, Fortnox will force the delivered quantity to zero. This can cause invoice amounts to show as zero. Either disable the warehouse module, ensure positive stock, or enable negative stock balances in Fortnox settings.
Getting started
The setup follows five steps: connect your Fortnox and ecommerce accounts, choose which data flows to activate, configure the field mapping and account rules, run a test sync to verify everything, and go live. Junipeer provides guided onboarding and support via chat and email throughout the process.
The Fortnox connector costs €74.5 per month excluding VAT and includes all sync flows.