Fortnox integrations for ecommerce

What can be integrated with Fortnox?

Fortnox is Sweden’s most widely used accounting system for small and mid-sized businesses. Via Junipeer, Fortnox connects with:

Ecommerce platforms: Shopify, WooCommerce, Magento, Centra, Norce, Shopware, Brink Commerce

Payment providers: Klarna, Stripe, Adyen, Svea, Qliro, PayPal

Carriers: nShift, Sendify

Warehouse management (WMS): NoWaste and other 3PL solutions

Each integration handles specific data flows — you choose which ones to activate.

What data syncs with Fortnox?

A typical Fortnox integration for ecommerce handles the following:

From ecommerce to Fortnox:

• Orders — each order creates an invoice in Fortnox with the correct sales account, VAT code, and payment method
• Credit notes — refunds and returns create credit notes linked to the original invoice
• Customers — new customers are created automatically in Fortnox with company details and payment terms

From Fortnox to ecommerce:

• Stock levels — inventory updates from Fortnox to the webshop in near real-time
• Articles — product data, prices, and SKUs are driven from Fortnox to the store

Payout reconciliation:

• Payouts from Klarna, Stripe, Adyen, and Svea are matched automatically against invoices in Fortnox
• Transaction fees are booked as write-offs on dedicated accounts

Fortnox and OSS VAT

For ecommerce businesses selling to EU customers, OSS (One Stop Shop) requires that sales to each EU country are booked with that country’s VAT rate on the correct sales account. Junipeer supports OSS mapping per EU country directly in the configuration, so every webshop order automatically lands on the right account with the right VAT code in Fortnox.

Should every Shopify order be its own invoice in Fortnox?

Yes — and this is one of the most common questions from Swedish ecommerce businesses. Creating one invoice per order (rather than aggregated bookkeeping) gives you:

• Full traceability — each order maps to a specific invoice, making it straightforward to handle disputes, refunds, and audits
• Correct OSS VAT — each EU country’s VAT rate is applied at the invoice level, not averaged across an export
• Accurate payout reconciliation — Klarna and Stripe settle by order, so per-order invoices make reconciliation automatic rather than manual
• Clean bookkeeping — your accountant (or Fortnox’s own AI categorization) works best with individual invoices, not lump sums

The one exception: very high-volume merchants (thousands of orders per day) sometimes prefer aggregated bookkeeping to keep Fortnox manageable. This is a configuration choice in Junipeer.

What is the difference between Fortnox Marketplace and Junipeer?

Fortnox Marketplace lists certified integration partners — including Junipeer. That is where you find and activate the integration.

Junipeer as a platform additionally gives you:

• Per-transaction logging — see exactly what happened with every order
• Automatic retries — failed syncs are retried automatically
• Error notifications — you receive an alert if something needs attention
• Support for multiple systems — connect Fortnox to multiple webshops or payment providers from a single platform

What does a Fortnox integration cost?

Pricing for Junipeer integrations with Fortnox:

• Fortnox connector: €74.50/month
• Shopify connector: €24.50/month
• WooCommerce connector: €14.50/month
• Fortnox integration license: 149 SEK/month (mandatory, covers all integrations)

Setup takes about 15 minutes and requires no coding.

Which Fortnox account plan do I need?

You need a Fortnox account with the Integrations module activated. This is a separate add-on in Fortnox (149 SEK/month) that enables API access for third-party integrations. Without it, no integration — including Junipeer — can connect to your Fortnox account.

The integration module is available on all Fortnox plans. If you’re unsure whether yours includes it, check under Settings → Integrations in your Fortnox account.

How to get started

1. Make sure your Fortnox account has the Integrations module activated
2. Create a Junipeer account
3. Connect Fortnox via API authentication
4. Connect your ecommerce platform
5. Choose which data flows to activate
6. Configure mapping — sales accounts, VAT codes, payment methods
7. Run a test sync and verify
8. Go live

Read more in specific guides: Connect Shopify with Fortnox | Bookkeeping Shopify in Fortnox | Integrate ecommerce with ERP