Shopify Payments vs Mollie: which should a Belgian store choose?

Mollie vs Shopify Payments: on a Shopify store, Shopify Payments is almost always cheaper, because Shopify adds a fee of 0.2% to 2% on top of every Mollie transaction. Mollie does win when you need payment methods Shopify Payments doesn't offer, sell on several platforms or can't use Shopify Payments (yet).

Both are good payment providers. The right choice depends on your Shopify plan, your average order value and the payment methods your customers use. Below we do the maths with Shopify's own rules. The bigger picture is in our guide to Shopify payments in Belgium and the Netherlands.

What is the difference between Mollie and Shopify Payments?

Shopify Payments is Shopify's built-in payment solution, with Stripe as the processor behind the scenes. You activate it in your admin and see payouts and chargebacks next to your orders. Mollie is an independent payment provider from Amsterdam that also works with WooCommerce, Magento and custom builds. On Shopify you connect Mollie with a separate app per payment method.

The rates per method are close. The biggest difference lies in how Shopify treats providers that aren't Shopify's own.

Mollie vs Shopify Payments: the rates side by side

These are the public standard rates for online payments in Belgium (checked in October 2026). Negotiated volume rates are not included.

On cards, Mollie is cheaper than Shopify Payments on Basic, equal on Grow and more expensive than Advanced and Plus. On Bancontact and iDEAL | Wero the fixed amounts are almost the same. Do watch the country of your Mollie account: with a Dutch account you pay 1.40% + EUR 0.25 for Bancontact. On an order of EUR 80 that is EUR 1.37 instead of EUR 0.39.

All rates per plan, with worked examples, are in Shopify Payments fees and rates. Switching? Our guide on how to set up Shopify Payments in Belgium walks you through it.

The Shopify fee makes the difference

If you use a provider other than Shopify Payments on Shopify, Shopify charges a fee on top of what that provider asks: 2% on Basic, 1% on Grow, 0.6% on Advanced and 0.2% on Plus. Shopify calculates it on the full order value, including VAT and shipping, and doesn't refund it when you refund an order.

Shopify Payments, Shop Pay, manual methods such as bank transfer and POS orders are exempt. So is PayPal, but only when Shopify Payments is your primary provider. Bancontact, iDEAL or Klarna through Mollie are not on that list: the rule applies to every transaction through an external provider.

Worked example: what does Mollie on Shopify really cost?

A Belgian store on the Grow plan gets 1,000 orders a month at an average of EUR 80, EUR 80,000 in revenue. 60% pay with Bancontact, 30% with a European consumer card and 10% with Klarna.

Without the fee both would cost almost the same: EUR 1,015 against EUR 1,025. With the fee, Mollie costs you EUR 810 more per month, almost EUR 9,720 a year. On Basic the gap is bigger, on Plus smaller.

It matters for a small store too. In our simulator, a store on Basic with 110 orders of EUR 100 and the average Belgian payment mix pays EUR 2,556 a year with Shopify Payments and EUR 5,142 with Mollie, of which EUR 2,640 is the Shopify fee. Run your own mix below.

Where Mollie wins

More payment methods for the Benelux. Through Mollie you can offer in3, Riverty, Billink, the KBC/CBC and Belfius bank buttons, SEPA bank transfer and Belgian meal and eco vouchers. Shopify Payments doesn't have them.

One provider for several platforms. If you also sell through WooCommerce, a custom build or a booking system, Mollie gives you one contract, one dashboard and one payout.

When Shopify Payments isn't available (yet). Shopify Payments needs a business and bank account in a supported country and doesn't approve every sector. For iDEAL | Wero, Shopify first reviews whether your store qualifies. Onboarding at Mollie is fast.

You can take it with you. If you move away from Shopify later, your Mollie account keeps working.

Negotiated rates. Mollie offers volume discounts on request. At high volumes on Plus, where the fee is only 0.2%, that can tip the balance. In that case, run both options with your real numbers.

Where Shopify Payments wins

No fee. In most worked examples that is the biggest difference.

Everything in Shopify. Payouts, refunds, chargebacks and fraud analysis are in your Shopify admin. With Mollie you manage the money and your bank account in the Mollie dashboard.

Fast checkouts. Shop Pay, Apple Pay and Google Pay are switched on automatically.

PayPal without the fee. That holds as long as Shopify Payments is your primary provider.

Lower rates on higher plans. On Advanced and Plus the card rates are lower than Mollie's standard rate. On Shopify Plus Bancontact drops to EUR 0.29 and iDEAL | Wero to EUR 0.15.

Lock-in: how tied are you?

Shopify Payments only works on Shopify. If you move to another platform, you need a new provider. Mollie is platform independent: your account, history and payouts stay when you switch platforms.

The real risk lies in saved cards and subscriptions. Stored payment details belong to the provider that processes them. When you switch, you have to migrate them or ask customers to pay again. Plan that separately if you sell subscriptions.

Can you use Shopify Payments and Mollie together?

Yes, in two ways, and both come at a price.

Shopify Payments as primary, Mollie for one extra method

You keep Shopify Payments for cards, Bancontact, iDEAL | Wero and Klarna, and install one Mollie app for a method Shopify Payments doesn't offer, such as in3. On those transactions you pay the Mollie rate plus the fee. An in3 order of EUR 80 on Grow costs 3.99% + EUR 0.95 (EUR 4.14) plus the 1% fee (EUR 0.80), EUR 4.94 in total.

Mollie for cards, Shopify Payments next to it

Shopify allows at most one direct external provider next to Shopify Payments. If Mollie processes the cards, with the fee, Shop Pay and the local methods run through Shopify Payments at the standard rate plus 1.25%. In our example of 1,000 orders that costs about EUR 1,955 a month: more than both other options. Plus merchants with a signed contract can't use this setup.

You can only have one card provider at a time. If you activate cards through Mollie, Shopify Payments no longer processes cards.

How to connect Mollie to Shopify

Create a Mollie account and have it verified.

In the Mollie dashboard, activate the payment methods on the right website profile.

Find the Mollie app for each method in the Shopify App Store, for example Mollie Bancontact or Mollie in3. Mollie recommends a separate app per method, so customers see them separately in the checkout.

Choose Install app and then Connect via Mollie. You need the owner role in both Shopify and Mollie.

Choose your website profile and activate.

Place a test order per method and check a refund from Shopify.

Don't simply delete an old Mollie app: according to Mollie, you then can't refund older payments any more. Deactivating is safe. Mollie methods also capture payments immediately, even when your store uses manual capture. For Klarna and other forms of buy now, pay later, capture does follow your Shopify settings.

Mollie or Shopify Payments: the decision guide

Is your product allowed on Shopify Payments? Often not for cannabis-related products, tobacco, gambling, adult or crypto. Then choose Mollie or another provider.

Do you sell on several platforms and want one provider? Then Mollie makes sense. Count the fee on your Shopify revenue.

Is Shopify Payments not active for your store yet? Start with Mollie for now and plan the switch.

Do you need a method Shopify Payments doesn't have? Think in3, Riverty or a bank button. Keep Shopify Payments as primary and add one Mollie app.

Are you on Plus with a negotiated Mollie rate? Run both with your real numbers.

None of the above? Choose Shopify Payments.

For our clients, four things weigh most: which methods your customers expect, the cost, the habits in your team and the integration with your accounting. For smaller businesses it's a matter of cents per order. For large merchants the difference between providers quickly reaches EUR 10,000 a month.

Payment fees are only one part of your budget. Also look at what a Shopify store costs in total.

What we learned in the Shopify Community

Klarna through Mollie got 2% extra. A Dutch merchant saw a 2% Shopify fee on top of Mollie's Klarna rate. That's correct: the fee applies to every external provider. Klarna is now part of Shopify Payments in Belgium and the Netherlands, so for Klarna the problem is outdated. Our take: buy now, pay later is less relevant for many of our clients, especially with high tickets, because the percentage fee adds up quickly. Source: Shopify Community, September 2023.

iDEAL not available for a new store. A merchant couldn't activate iDEAL through Shopify Payments and connected Mollie, after which iDEAL worked right away. Later replies point to the 2% fee on Basic. A fixed threshold of 100 orders, which some mention, isn't confirmed by Shopify. Source: Shopify Community, September 2025.

Bancontact disappeared from the checkout. A Belgian store saw Bancontact through Shopify Payments disappear a week before launch. Support suggested Mollie as a temporary replacement; the thread is unsolved. Our take: we don't set up a standard backup provider. We do always make sure there is more than one payment method. Source: Shopify Community, August 2024.

Money from Mollie Bancontact runs outside Shopify. A Belgian merchant couldn't find where to change the bank account for Mollie Bancontact in Shopify. Shopify referred them to Mollie: you manage that money in the Mollie dashboard. Source: Shopify Community, June 2024.

How 6th Man helps

We set up both Shopify Payments and Mollie, so we have no stake in either. We run your real payment mix, tell you honestly when Mollie fits better and set up the chosen setup, including testing and refunds. Start with our payment simulator for e-commerce managers and talk the result through with us.