This guide is for shop and finance staff connecting Mollie to Fortnox through Junipeer. It covers the flows, the connection, how payouts are booked and matched, and what to check before going live.
Work through Connecting payment services to Junipeer first. It covers the steps every payment provider shares. This guide covers what is specific to Mollie and Fortnox.
What the integration does
The Mollie ↔ Fortnox integration has two flows. Both read from Mollie and write to Fortnox.
Flow | What it does |
|---|---|
Export Payouts to Fortnox | Reads Mollie payouts, matches each transaction to its Fortnox invoice, marks the invoice as paid and books the fees. |
Export Orders to Fortnox | Creates orders (and optionally invoices) in Fortnox from Mollie orders. |
Choose your flows carefully. If your orders already reach Fortnox through a webshop integration (for example Shopify, Centra or WooCommerce), do not turn on Export Orders to Fortnox here — you would get duplicate orders. Use this integration for payouts only.
Turn on Export Orders to Fortnox only if Mollie is where your orders come from and nothing else sends them to Fortnox. That flow has its own order, customer, article, shipping and sales-account settings, much like a webshop integration. See Order sync for how order settings work.
Before you start
Fortnox is prepared: an integration user, currencies, VAT rates, sales accounts and a payment method for Mollie. See Prepare Fortnox for integration.
You have access to your Mollie account.
You know which Fortnox accounts to use for fees, VAT on fees and rounding. Ask your bookkeeper.
Connecting Mollie and Fortnox
In the Junipeer app, go to Get Started → Connect Systems.
Connect Fortnox by clicking the Fortnox button and logging in. Use the Fortnox user with the right permissions.
Connect Mollie and follow the steps shown in the app.
Check that both systems show a green checkmark.
Choose the Mollie balance
Under the Payout section, set Which Balance should we load transaction from? This is required. Junipeer loads payout transactions from the balance you choose. The list shows the balances in your Mollie account, for example one balance per currency.
Only one balance per integration is supported. If you need several, contact Junipeer support.
If the list is empty, check that Mollie is connected. An empty list almost always means the connection, not the setting.
Booking settings for payouts
Open Configure → Settings and find Booking Accounting Settings for Settlements. Add Mollie as the payment provider and fill in the accounts below. This decides how each payout is booked in Fortnox. Without it, payouts will not book correctly.
The account numbers below are the usual Swedish examples shown in the app. Confirm every account with your bookkeeper before you save — your chart of accounts may differ.
Setting | What to enter |
|---|---|
Payment Method | The payment method (betalsätt) in Fortnox for Mollie. Required. The list is read from Fortnox — if Mollie is missing, add it in Fortnox first. |
Map Currency with Mode of Payment (if different than (default) Payment Method above) | Optional (advanced). Use a different Fortnox payment method for payouts in a certain currency, for example EUR payouts that go to a separate EUR account. Currencies you don't map use the Payment Method above. |
Account Number Bank Costs | The account for Mollie's fee, excluding tax. Required. The app suggests 6570. |
VAT account for provider fees | Where VAT on Mollie's fees is booked. This is input VAT you can deduct. Required. Only used when Mollie reports VAT on a fee. The app suggests 2641 in Sweden. |
Account Number for Incoming Tax | Only used when the payout isn't from Sweden. Leave empty for Swedish payments. |
Account Number for Penny rounding | Small differences between the invoice amount and the paid amount. Required. The app suggests 3740. |
Account Number for Currency Profit | Optional. Small differences caused by currency conversion that give a profit. The app suggests 3960. Leave empty to use the penny rounding account for both profit and loss. |
Account Number for Currency Loss | Optional. The same for a loss. The app suggests 7960. |
Click the ? next to each setting in the app for more details.
How payouts are matched to invoices
How a payout is reconciled
From the customer's payment to the right account in your ERP.
Matching relies on the reference saved on the order or invoice when the order was synced. Without the reference the payout cannot be matched.
When Mollie pays out, Junipeer reads the payout and finds the Fortnox invoice for each transaction. Matched invoices are marked as paid, and the fees are booked to the accounts you set above.
To find the right invoice, Junipeer takes a reference from the payout and searches for it in a field on the Fortnox invoice (or order). You decide where it looks under General Settings:
Setting | What it does |
|---|---|
Payout Reference Field | Required. The Fortnox field that holds the reference, usually the shop order ID or the payment order ID. In many setups this is ExternalInvoiceReference1. Open a recent invoice in Fortnox to see which field holds the order reference. |
Fallback Payout Reference Field | Optional (advanced). A second field to try if the reference isn't found in the first one, for example ExternalInvoiceReference2. |
Use Payment ID as Payout Reference | Optional (advanced). By default Junipeer searches for the merchant reference (usually your order number). Choose this to search for the payment ID instead (usually the Mollie order ID), or to try one and then the other. Pick what is actually stored in your Payout Reference Field. |
Search for the Payout Reference on the Order | Optional (advanced). Yes searches on the Fortnox order and then finds its invoice. No searches directly on the invoice. |
Book keep invoice payment | Optional (advanced), default Yes. Books (bokför) the payments Junipeer creates from payouts. Keep it on Yes if invoices should be marked as paid automatically. |
Read more in Matching payout references in Fortnox and Payout reconciliation.
Going live
Payouts are usually not something you can test in advance. The scheduled run must run in production, and you should check the results after each run.
Fortnox is connected and prepared, including a payment method for Mollie.
Mollie is connected and Which Balance should we load transaction from? is set.
The right flows are on: Export Payouts to Fortnox, and Export Orders to Fortnox only if no other integration sends your orders.
Booking Accounting Settings for Settlements is filled in for Mollie, and your bookkeeper has confirmed the accounts.
Payout Reference Field matches the field your orders' reference is stored in. Check one recent Fortnox invoice.
If you use the orders flow, test one or two orders with the test panel first.
Schedule Export Payouts to Fortnox. Payouts are usually run once a day, for example at 23:00.
Contact your Junipeer onboarding contact to review the setup before you go live.
After the first payouts, check in Fortnox that invoices are marked as paid and that fees are booked to the right accounts.
Common pitfalls
Orders flow on in two places. Running Export Orders to Fortnox here while a webshop integration also sends orders gives duplicates.
Wrong balance. If payouts are missing, check that the selected balance is the one your payouts are paid from. Only one balance is read.
"No invoice found" on a payout. Usually the Payout Reference Field points to a field that is empty or holds a different reference than the payout carries. Open the failing task in the logs, note the reference, and check which Fortnox field holds it. The invoice may also not exist yet, if the payout arrived before the order was synced.
The payment method is missing from the list. Create it in Fortnox first, then click Clear Cache on the settings page.
Payment date before invoice date. Fortnox can reject a payment dated before the invoice. See Error codes.
Invoices in another currency than the payout. This gives "Unsupported currency combination". If you sell in several currencies, contact Junipeer support to set it up.
New payment provider switched on in the webshop before Junipeer was configured. Payouts for those early orders can get wrong references. Configure Junipeer first. If it already happened, contact support.