What needs to be recorded?
When you sell through Shopify, several types of transactions need to end up in Fortnox:
Sales and VAT — each order represents revenue that should be posted to the correct sales account with the right VAT code.
Shopify fees — Shopify charges transaction fees on every sale. These should be recorded as an expense, typically on a bank fees account.
Payouts — Shopify aggregates your sales and pays out the net amount (sales minus fees) to your bank account. The payout needs to be matched against the invoices in Fortnox.
Returns and credit notes — when a customer returns a product, a credit note needs to be created in Fortnox linked to the original invoice.
Shipping charges — if you charge the customer for shipping, it's recorded separately.
How it works manually
Without an integration, most merchants record Shopify sales like this:
1. Export orders from Shopify 2. Create invoices manually in Fortnox for each order 3. Verify that VAT codes and sales accounts are correct 4. When Shopify makes a payout, match the amount against the relevant invoices 5. Record the Shopify fee as a separate expense
This works at low volumes. But at 30–50 orders per month, it becomes time-consuming and error-prone.
Automate with an integration
With a Junipeer integration, bookkeeping happens automatically:
Orders → create invoices in Fortnox with correct VAT codes, sales accounts, and amounts.
Fees → recorded separately on your chosen expense account.
Payouts → automatically matched against the invoices they cover.
Returns → credit notes created automatically linked to the original invoice.
You configure the account mapping once and everything flows automatically after that.
Connect Shopify with Fortnox →
Common mistakes to avoid
Forgetting the Shopify fee — Shopify deducts the fee from the payout, but it needs to be recorded as a separate expense. Otherwise your revenue figures won't be accurate.
Confusing payouts with sales — the payout from Shopify is not the same as the sales amount. The payout is sales minus fees, sometimes with returns deducted.
Wrong VAT code for EU sales — if you sell to consumers in other EU countries, each country needs the correct VAT rate under OSS rules.
Next steps
Need help connecting Shopify and Fortnox? Read our Shopify–Fortnox setup guide or see all Fortnox integrations.
Want to try it? Start a free trial — basic setup takes about 15 minutes.