How to Connect Mollie to Shopify: Apps, Methods and Fees

How Mollie Connects to Shopify

Mollie doesn't plug into Shopify as one gateway setting. It comes as a set of apps on the Shopify App Store, published by Mollie B.V., and each app adds one payment method to your checkout: one for iDEAL, one for Bancontact, one for cards, and so on.

Mollie's installation guide tells you to install each method you want to offer individually, and gives the reason:

The exception is Mollie ‑ Payments, whose listing offers all Mollie payments in a single app; that is the grouped checkout the quote warns about. Whichever you pick, each installed app shows up in Settings > Payments, where you open it with Manage to switch on test mode or contact Mollie.

One thing the app model can't do is mirror Shopify. Mollie's getting-started page warns that a method might be available via Shopify itself but not for this specific integration, so check that Mollie has an app for every method you plan to offer.

Which Mollie App to Install for Each Method

The table lists the main methods for stores selling in the Netherlands and Belgium, the Mollie app for each, and whether Shopify Payments already offers the method to a store based in the Netherlands.

Shopify Payments shows its local methods by the customer's location, not your store's, so a Netherlands store with Bancontact turned on offers it to shoppers in Belgium. Where the third column says yes, read the section on running both providers before you install the Mollie version.

Can You Use Mollie Alongside Shopify Payments?

Shopify answers the basic question on its third-party providers page:

That quote is about a third-party card provider. Shopify also keeps additional payment methods separate from the credit card payment provider in Settings > Payments, so Shopify Payments can keep cards, Shop Pay and its local methods while Mollie apps add the methods it doesn't offer. The quoted page is just as clear that Shopify's third-party fee doesn't go away: third-party transaction fees apply to all transactions processed through third-party and alternate payment gateways, even when Shopify Payments is activated.

The route without Shopify's third-party fee on card payments is Shopify's own. Its additional-payment-methods page says that to avoid third-party transaction fees for credit card payments, you activate Shopify Payments.

One iDEAL Button, Not Two

iDEAL | Wero is a Shopify Payments local method for customers in the Netherlands, and Bancontact is one for customers in Belgium. Shopify's rule for local methods is that you must deactivate any conflicting additional payment gateways before you can activate them.

The rule names no specific gateways. The safe order is to decide first which provider runs each method, then turn that method on in one place only.

Mollie's side says little here: apart from its warning that Onsite Cards overrides your store's default payment methods, the Mollie Shopify pages we read don't mention Shopify Payments (what we read).

Before you install Mollie's iDEAL or Bancontact app on a store that runs Shopify Payments, check which local methods Shopify Payments already offers your customers.

What Shopify's Pages Don't Settle for Mollie

Shopify sorts card providers into two types: direct providers, where the customer pays on your online store, and external providers, where the customer finishes on a checkout page hosted outside it.

When a direct provider runs alongside Shopify Payments, the third-party provider stays primary for card payments, and Shopify says transactions it processes itself, such as Shop Pay and local methods, are charged at standard Shopify Payments rates plus a 1.25% premium.

Which side of that line Mollie falls on is the open question: none of the pages we read classifies Mollie's apps as direct or external, so whether the premium applies to your mix of Shopify Payments and Mollie isn't established here.

While the documentation is silent, ask the people who bill you. Shopify's own advice for rates is to check the pricing page or contact Shopify Support for your location. For the app side, contact Mollie from your admin: Settings > Payments, open the method with Manage, then Contact Mollie - [method].

What You Need Before You Connect Mollie

The first check decides whether Mollie will process payments for you at all. The second decides whether a given method appears at checkout. They fail in different places, so it pays to keep them apart.

Gate One: Mollie Approves Your Business

Most stores won't pay to join. Mollie charges an onboarding fee only to businesses in a few listed categories, such as charities and crowdfunding, and says that if your business is not in one of these categories, you will not be charged this fee.

Gate Two: The Method Shows at Checkout

Shopify words the last row from its side: after you activate an additional payment method, your customers can use it at checkout when the method is available for their market and meets provider requirements. So a method can be fully set up and still not show to every shopper.

Limits to Check Before You Commit

• One base currency. Mollie's app checks your store's base currency to decide which methods you can install, and it doesn't support multicurrency. Mollie says the only way to offer a currency-specific method is a separate Shopify store with that currency as its base currency.
• Manual capture: Mollie's guide points both ways. It says Mollie's payment methods always settle payments automatically, even if your store is set to manual capture; its card section says Mollie supports Shopify's separate payment authorization and capture; and its app uses Shopify's native capture settings to decide when to settle Klarna/BNPL payments.
• Klarna in Scandinavia and the UK. There, Mollie accepts Klarna only in the currency of the Scandinavian or UK country set as your store's address.
• No pre-orders with local methods. Shopify's pre-order setup page says customers can't use local payment methods such as Klarna and mollie iDEAL | Wero to purchase pre-orders.
• Subscriptions need a partner app. Mollie names FirmHouse as its subscriptions integration. Later payments go on the same card if the first payment was by card, and by SEPA Direct Debit otherwise. For iDEAL, whether shoppers can pay for subscriptions with it has its own answer.
• Several business entities. If you sell with multiple entities, Shopify asks you to confirm that the additional payment method app supports the market and the assigned business entity.

How to Connect Mollie to Shopify, Step by Step

Steps 1 to 3 come before any install; step 4, installing the app, is where two routes start. Mollie's guide starts on the method's App Store listing, with Add app and then Install app in your admin. Shopify's Help Center starts in the admin: go to Settings > Payments, search for the provider, click Activate and then Install app. Both routes end with the same app in your store.

In the admin as of November 10, 2026, the provider search sits behind a + Method button in a section called More ways to pay; the Help Center calls that button Add payment methods.

In Shopify adminOpen in your store

1. Settings
2. Payments

Zoom

The button opens an Add payment method page with two tabs, Search by payment method and Search by provider; Mollie is a provider. Shopify asks you to pick providers that are compatible and available in your region, so check Mollie's country list before you search.

In Shopify adminOpen in your store

1. Settings
2. Payments
3. Add payment method

Zoom

From Mollie's side, open the listing for the method you want, check that the developer is Mollie B.V., and install it.

Shopify App Store listing for Mollie - iDeal

Zoom

The checklist runs in the order Mollie's guides set out, with the + Method button and Search by provider tab our test admin showed as of November 10, 2026. Steps 3 to 7 repeat for every extra method, because each method is its own app; then clear Enable test mode on that method too, as in step 8.

Mollie's test and go-live guide covers steps 7 and 8. In test mode, Mollie simulates payments, so no real money transfers occur.

Card Payments: Credit Card App or Onsite Cards

For card payments Mollie has two apps. Mollie ‑ Credit Card lets you choose which card logos appear: in Settings > Payments, open it with Manage and tick at least one card brand. Mollie suggests hiding cards to avoid higher transaction fees or regional restrictions.

Onsite Cards is the newer app. Mollie says it collects card details directly in Shopify checkout, with no need to redirect buyers to an external payment page.

Mollie's Onsite Cards setup has a step for existing merchants: they will need to deactivate the existing Cards app and install the new Onsite Cards app. It sets one rule for the old app:

What Mollie on Shopify Costs: Two Fees per Order

Mollie's apps are free to install. What you pay sits on two separate bills: Mollie charges its rate per successful payment, and its iDeal listing, like its card and Bancontact listings, notes that external charges may be billed by Mollie B.V. separately from your Shopify invoice. Shopify then adds its third-party transaction fee on top.

Mollie's Rates for the Methods Dutch and Belgian Shoppers Use

Mollie describes its standard pricing as no minimum costs, no lock-in contracts, no hidden fees, charged only on successful transactions, and offers volume discounts to businesses processing over €100k a month.

The Mollie pages we read name no fee for the Shopify connection itself on top of these rates (what we read).

Shopify's Third-Party Fee on Top

Shopify's fee depends on your plan. Its Dutch pricing page lists the third-party rate at 2% on Basic, falling to 1% on Grow, 0.6% on Advanced and 0.2% on Plus.

It comes in addition to Mollie's fee, and Shopify calculates it on the products minus discounts, plus tax and shipping, so the base is the whole order total.

Take one €100 order, tax and shipping included, paid with iDEAL | Wero through Mollie. Here is what the two fees add up to on each plan:

Mollie's iDEAL | Wero rate on its English and Dutch pricing pages as of November 10, 2026 (€0.42 on its German, Austrian, French, Spanish and Italian pages), plus Shopify's third-party transaction fee by plan.

On this €100 order, Shopify's share is the bigger part of the bill on every plan but Plus. Mollie's iDEAL fee is flat, while Shopify's is a percentage, so the larger the basket, the wider that gap.

Whether Shopify's fee justifies a plan upgrade or a move to Shopify Payments depends on your volume; our gateway guide works through the surcharge and when Shopify waives it.

Refunds, Chargebacks and Payouts

Mollie's Shopify page says you can process full or partial refunds directly from your Shopify admin. Its general help adds the rules: refunds are possible for every method except gift cards and Paysafecard, credit card refunds must be made within one year of the transaction, and Mollie processes a refund the next business day.

What a refund made in Shopify looks like inside your Mollie account is something the Mollie pages we read don't describe beyond the one line on Mollie's Shopify page (what we read).

Mollie can also refund a payment by itself. When Shopify can't confirm a transaction, for example because a product is out of stock or a discount code is no longer valid, the integration automatically issues a refund to prevent any incorrect charges.

Chargebacks run through Mollie. If the card issuer accepts one, Mollie deducts the transaction amount and a chargeback cost from your available balance. Mollie's pricing page prints no card chargeback fee; Mollie shows the fees that apply to your account under each payment method's Pricing & info in your Mollie Dashboard, and its dispute-fee article puts the standard fee for a lost Klarna dispute at €25. Klarna adds up to €30 on top of that standard fee when your overall dispute rate exceeds 1.5%, the same article says.

Payouts come from Mollie too. Mollie pays out weekly by default, and weekly and monthly payouts are free. If you process less than €500,000 a year, daily and manual payouts are free for the first 5 each month and then cost €0.25 each (multi-currency payouts, payouts to a Mollie Business Account and some account types are exempt), per Mollie's help center as of November 10, 2026; the FAQ on its pricing page says it doesn't charge extra for daily payouts.

A payment first settles to your Mollie balance after a delay that depends on the payment method, and your payout schedule then decides when that balance is sent to your bank.

You can change how often you're paid in Mollie under Settings > Balance once your account has been reviewed and payouts have been enabled, but Mollie notes that changing your payout frequency does not affect how quickly payments settle. A payment in a currency you haven't added to your Mollie account is converted to your primary currency before it's paid out.

When a Mollie Method Doesn't Show or a Payment Fails

For anything else, contact Mollie from your admin: Settings > Payments, open the method with Manage, choose Contact Mollie - [method] and describe the problem.

One more thing to expect on new orders: Shopify says that, to keep information synchronized between Shopify and some additional payment providers, activity on orders that are pending payment might be restricted.

The Bottom Line

For a Dutch or Belgian store already on Shopify Payments, Mollie fills gaps. For a store without Shopify Payments, Mollie can run cards and the methods it lists for Shopify.

Frequently Asked Questions