Shopify Fortnox integration — orders, invoices, credit notes and payouts
Every Shopify order becomes an invoice in Fortnox. Refunds become credit invoices. Payouts from Shopify Payments, Klarna, Adyen and Svea are reconciled automatically against the right invoice. OSS VAT is handled per EU country.
Starting from €99/month →Ideal for
For merchants selling via Shopify and booking in Fortnox. Fits both B2C stores that want to automate daily sales bookkeeping and B2B stores that need individual invoices per customer. Especially valuable for stores selling into multiple EU countries that need OSS handling, or using multiple payment providers where manual payout reconciliation takes hours each week.
Why Shopify–Fortnox automation is worth it
- ×Manually invoicing each Shopify order takes 5–15 minutes per order and doesn’t scale as volume grows
- ×Stock levels in Shopify lag reality in Fortnox — the result is overselling during campaigns and frustrated customers
- ×OSS sales to the EU require the right sales account and VAT rate per country. Manual bookkeeping quickly becomes a source of errors at tax audit
- ×Payouts from Klarna, Shopify Payments and Adyen arrive as lump sums that must be reconciled against hundreds of individual invoices — work that easily takes half a day each week
Junipeer connects Shopify to Fortnox with full automation of the order flow, invoicing, refund handling and payout reconciliation. The Shopify order creates an invoice in Fortnox with the right sales account, VAT code and payment method. When the customer’s payment arrives via Shopify Payments or a third-party provider, the payout report is reconciled automatically against the corresponding invoice, and provider fees are booked as write-offs. Refund in Shopify? Credit invoice in Fortnox, linked to the original. Setup takes about 15 minutes — after that you configure the data mapping to match your chart of accounts and your payment methods.
Benefits
- ✓Every order is booked with the correct sales account, VAT code and OSS country — no manual invoicing in Fortnox
- ✓Payouts from Shopify Payments, Klarna, Adyen and Svea are reconciled against invoices automatically. Provider fees are booked as write-offs
- ✓Refunds create credit invoices linked to the original invoice. Fortnox bookkeeping reflects store reality in real time
- ✓Stock levels in Fortnox drive what shows as available on Shopify — no overselling during campaigns
How it works
Connect your systems
Connect Fortnox and Shopify via secure authentication — no technical expertise needed, takes about 15 minutes. Requires an active integration license in Fortnox.
Choose what to sync
Activate the flows you need: orders, articles, stock, customers, refunds, payouts. Each flow can be run separately and paused at any time.
Map your data
Map Shopify orders to the right sales accounts in Fortnox (typically the 3000-series), match payment methods to Fortnox payment types, and configure OSS mapping per EU country.
Run a test sync
Sync a few test orders to verify that accounts, VAT and shipping mapping are correct. Review the log and adjust before going live.
Go live
Activate continuous synchronization. The monitoring dashboard shows status per flow and alerts if anything needs attention.
See it in action
Pricing
FAQ
Trusted by
CLN Athletics
"We wanted a setup that supports our brand experience from start to finish. With R3 and Junipeer, everything is connected — orders, payments, and accounting."
— Simon Hallberg, E-commerce Manager
USWE Sports
"I've been really happy with how easy everything was to get going. Junipeer gave us great support from the start, and the whole process from setup to live integration went faster than I thought it would."
— Fredrik Gustafsson, CMS & System Manager
Butterick's
"Sweden's oldest party retailer integrated Shopify with Fortnox to sync product data, inventory, orders, and financials — reducing manual work significantly."
— Butterick's
A Retro Tale
"Using Junipeer will save us tons of hours from manual bookkeeping and this helps us to scale faster."
— Daniel Tidebrink, CEO
VOID Cycling
"This kind of integration is priceless to us. The team at Junipeer was more than helpful and fast, so we could be up and running in no time."
— Fredrik Gustafsson, CMS & System Manager
Folkness
"Junipeer supported the process and ensured a smooth transition by integrating Shopify with Fortnox. The setup delivers the functionality we needed."
— Henrik Samhag, Co-Founder
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Last updated: March 2026