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Mollie integration

Mollie, the Dutch payment provider, processes your payments, but your money arrives later and as a single amount, with refunds, chargebacks and fees already deducted. Connect Mollie properly and you see per order whether it has been paid, and you reconcile every payout in your accounts without hunting around.

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4.8 from 127 reviews
ISO 9001 & 27001
MollieEcommerce and payments · Mollie B.V.
  • Payments and payment status goes back and forth with Your other systems
  • Refunds goes back and forth with Your other systems
  • Chargebacks goes back and forth with Your other systems
  • Payouts (settlements) goes back and forth with Your other systems
Your other systemsSuch as Moneybird

Built for clients including Tata Steel, M&G Investments, Digistore24, Toppers in Concert, Bar-le-Duc and Loogman

What you exchange

This is the data organisations most often let flow between systems. Which of it matters to you depends on where work is getting stuck today.

Payments and payment status

For each order, the payment status, such as open, paid, failed, expired or cancelled. Your online store or ERP only passes an order to the warehouse once it has actually been paid.

Refunds

Full and partial refunds, for example after a return. Mollie deducts the amount from your Mollie balance. If your balance is too low, the refund waits until there is enough on it again.

Chargebacks

A customer can dispute a payment through their bank or card issuer. If it is upheld, Mollie takes the money from your balance. Your integration flags the order and your accounts show the chargeback.

Payouts (settlements)

Mollie periodically pays out your balance to your bank account. For each payout you can see which payments, refunds and chargebacks it includes and which fees were deducted. That is exactly what you need to reconcile.

Customers, mandates and subscriptions

For recurring payments, Mollie stores customers and their authorisations (mandates). Link those to your CRM or subscription system and you know who is actively paying and whose direct debit has failed.

Popular integrations

For each combination: which data moves back and forth, what the standard integration does and what to watch out for.

Off the shelf or custom

Not always. If an existing integration for Mollie does exactly what you need, we'll tell you.

What already exists

Mollie builds its own integrations for Shopify and WooCommerce. For Shopify there is the Mollie Payments app by Mollie B.V., which also lets you refund from the Shopify admin. For WooCommerce there is the Mollie Payments for WooCommerce plugin, with full and partial refunds and support for WooCommerce Subscriptions. For taking payments in your online store, an integration like that is usually all you need.

Mollie's integrations overview also has a category for accounting and invoicing. Check whether your package is listed and what exactly the integration takes over: only the amount paid out, or also the individual payments, refunds and fees.

A standard integration usually stops at the edge of one system. The payment plugin knows your online store and the accounting integration knows your general ledger, but nothing compares the payout with your orders, returns and other channels. That's where the manual work is. We can integrate Mollie with any system, even when there is no standard integration for it.

When you need custom work
  • You want every payout reconciled automatically: the amount in the bank, broken down into payments, refunds, chargebacks and fees per order.
  • You use Mollie outside an online store, for example with payment links in your own software or a payment terminal, and the payment needs to land in your ERP.
  • You have several website profiles or companies and want one overview in your accounts.
  • Refunds need to start from your ERP or service system rather than from the online store.
  • You collect subscriptions through Mollie and your CRM needs to know who is actively paying.
How it works technically

REST API and keys

Mollie has a REST API. You start with an API key per website profile: a test key for building and a live key for real payments. For work at organisation level there are advanced access tokens with scopes, and OAuth for apps that act on behalf of other Mollie users. Mollie no longer recommends the Orders API and points to the Payments API instead.

Webhooks

When a status changes, Mollie calls your webhook with only the payment ID. Your integration then fetches the current status through the API, so a fake notification can never release an unpaid order. If your server doesn't reply with 200 OK within 15 seconds, Mollie retries up to ten times, spread over about 26 hours.

Signed webhooks

Mollie also has a newer type of webhook: messages with an HMAC-SHA256 signature in the X-Mollie-Signature header, and events for payments, payouts and balance transactions, among others. Some of the events are still in beta.

Balance and payouts

The Settlements API shows, for each payout, the bank reference, the payments, refunds and chargebacks, and the fees deducted. The Balances API gives an up-to-date overview of all transactions on your balance; Mollie recommends it for connecting Mollie to your accounting software. Data from before 1 July 2022 isn't included.

Test mode

In test mode you create payments without real money and choose the outcome yourself. You can also test refunds and chargebacks. Test data is kept separate from your live data. Testing only works in euros, and the settlement endpoints don't work in test mode.

AI in between

An integration moves data. In between, AI can read, sort and prepare a suggestion. Where it matters, a person decides.

Discrepancies in payouts

AI compares each payout with your orders and returns and reports what doesn't match, such as a chargeback without a matching order or a refund that looks like a duplicate. A team member reviews and posts it.

Customer questions about payments

For a question like 'did my payment go through?', an assistant looks up the status and answers straight away. Refunding remains a job for a person, or for a rule you set yourself in advance.

Suggested entries

Items that can't be matched automatically get a suggested order or general ledger account based on previous entries. Your bookkeeper approves or adjusts.

Where it goes wrong

Relying on the return to your store

A customer who closes their browser after paying never reaches your thank-you page. Always determine the status through the webhook and the API, not through the redirect. Mollie also advises against predicting yourself when a payment will expire.

Posting the payout as one revenue entry

If you post a payout as a single amount, you lose sight of fees, refunds and chargebacks. Post the parts separately, or your revenue per order will never reconcile.

Duplicate refunds

A timeout on a refund tempts you to try again. Send an Idempotency-Key with it: Mollie then recognises a repeated request within an hour as a duplicate and doesn't execute it again.

A webhook that replies too slowly

If your webhook does heavy work first, it goes over the 15 seconds and Mollie counts the delivery as failed. Reply immediately with 200 OK and process the payment afterwards in a queue.

How we build an integration

  1. What goes where

    Which data moves, in which direction, and which system wins when two values differ. That is written down before anything gets built. For this integration, that means: Payments and payment status, Refunds, Chargebacks, Payouts (settlements), Customers, mandates and subscriptions.

  2. Fields and rules

    For every field, how it translates between the systems: statuses, VAT codes, general ledger accounts, item numbers. And what happens with a duplicate or a missing value. For this integration, that means: REST API and keys, Webhooks, Signed webhooks, Balance and payouts, Test mode.

  3. Testing with real cases

    In a sandbox or test administration, with the exceptions you actually run into: credit notes, partial deliveries, changed customer details.

  4. Live, with logging and monitoring

    Every sync is logged, and when something fails, someone gets an alert. If a vendor changes its API, we update the integration.

The Your Tech Club team at the office in Amsterdam
Amsterdam
Who you'll talk to

No account manager. You talk to someone who builds integrations themselves, and who will tell you when a standard integration is enough.

Joey van VlietJoey van VlietFounder
Yassine SeghrouchniYassine SeghrouchniFounder
  • Office on the Duivendrechtsekade in Amsterdam
  • ISO 9001 and ISO 27001, certified by Kiwa
  • 500 projects delivered
  • 4.8 from 127 reviews
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Frequently asked questions

Can I connect Mollie to my accounting software?

Yes. Through the Settlements API and the Balances API you fetch, per payout and per transaction, what happened on your balance, including fees deducted. That lets you post a payout broken down and reconcile it against the bank transaction. First check whether your accounting package already has a Mollie integration and what it takes over.

What is the difference between a payment and a payout at Mollie?

A payment is what a customer pays you through Mollie. It lands on your Mollie balance first. A payout (settlement) is the amount Mollie transfers from that balance to your bank account, after deducting refunds, chargebacks and fees, among other things.

Do I need a separate plugin for Shopify or WooCommerce?

For taking payments in your store, you use Mollie's own integration: the Mollie Payments app in the Shopify App Store or the Mollie Payments for WooCommerce plugin. They handle checkout and refunds. For processing in your accounting software or ERP, you need a separate integration.

Can I test a Mollie integration without real money?

Yes. With a test key you create payments in test mode, separate from your live data. You choose whether a test payment succeeds, fails or expires, and you can test refunds and chargebacks. Testing only works in euros.

Why does Mollie only send an ID to my webhook?

So that nobody can mark an order as paid with a fake notification. Your integration uses the ID to fetch the current status from Mollie, with your own key. If your server is briefly unreachable, Mollie retries up to ten times, spread over about 26 hours.

Should I use the Orders API or the Payments API?

Mollie no longer recommends the Orders API and points to the Payments API. If you're building something new, use the Payments API. If your integration still runs on the Orders API, include the switch in your next round of maintenance.

Related services

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Sources

The technical facts on this page come from the vendors' official documentation, checked on 19 September 2026. Vendors change their APIs and limits; when we build an integration, we always check the current state.