SME Online Payments: Stripe vs Mollie Fees Compared (2026)

The verdict in three sentences

For EUR 1.2 million collected per year, switching payment provider or renegotiating your rate saves EUR 3,000 to 8,000 a year, for an integration of EUR 1,000 to 4,000 excl. VAT. Payplug is the cheapest on European cards above a certain volume, Stripe offers the most complete ecosystem, Mollie stands out for simplicity and the range of European payment methods. The right choice depends less on the headline rate than on your card mix, refunds and disputes.

Public 2026 rates on European cards

All three charge a percentage of the amount plus a fixed fee per transaction. The grids below are the public entry rates seen in 2026; above EUR 500,000 a year, all of them are open to negotiation.

Watch the extra fees: currency conversion (1 to 2%), advanced fraud screening at Stripe, refund fees on some plans. For an SME with a high return rate, these lines sometimes weigh as much as the main rate.

Simulation for EUR 1.2 million collected per year

Assumptions: average basket of EUR 120, i.e. 10,000 transactions a year, 100% European cards, 25 disputes a year. These are 2026 estimates on public rates, before negotiation.

The EUR 3,725 to 7,200 annual gap matches the expected range. If 20% of your customers pay with non-European cards, the gap narrows and Stripe's international edge can make up for it.

Switching provider without breaking checkout

Integration costs EUR 1,000 excl. VAT with a native module (PrestaShop, WooCommerce, Shopify), EUR 2,000 to 4,000 excl. VAT for a custom site, recurring billing or an ERP connection for accounting reconciliation. Plan for two sensitive points: migrating stored cards for subscriptions, which Stripe, Mollie and Payplug can transfer through a PCI DSS procedure, and bank reconciliation, whose format changes.

An effective strategy is to keep two providers: the cheapest for European cards, the other for international or installment payments. Routing happens on the site, with no impact on the customer.

Mini case study

Sophie, CFO of a garden equipment SME in Bordeaux, collects EUR 1.2 million a year online through Mollie, with an average basket of EUR 120. She asks for a comparison.

• Current Mollie cost: EUR 24,475 a year, an effective rate of 2.04%.
• Payplug offer negotiated at 1.2% + EUR 0.25: EUR 17,275 a year.
• Annual saving: 24,475 − 17,275 = EUR 7,200.
• Integration on her custom site and connection to the accounting software: EUR 2,500 excl. VAT.
• Payback: 2,500 ÷ 7,200 × 12 = just over 4 months.

She uses the switch to add pay-in-3, which lifts the average basket on products above EUR 400.

FAQ

Are Stripe rates negotiable?

Yes, from around EUR 80,000 to 100,000 collected per month, Stripe offers custom pricing. A cut of 0.1 to 0.3 points is common for a well-established SME.

Do we need a merchant agreement with our bank?

No with Stripe, Mollie or Payplug, which act as licensed payment institutions. A traditional bank remains an option, often with a EUR 20 to 50 monthly fee on top of commissions.

How long does switching provider take?

Allow 2 to 4 weeks, including 3 to 10 days of account verification (KYC) and one week of testing. The switchover itself happens without interrupting sales.

Does pay-in-3 cost more?

Yes, allow 2 to 4% of the amount paid by the merchant depending on the offer. It is justified on baskets above EUR 200 or 300, where it often lifts conversion by 10 to 20%.

How can we reduce disputes?

Enable 3D Secure on high amounts, show a clear bank statement descriptor and answer refund requests within 48 h. Each avoided dispute saves EUR 15 to 20 in fees plus the goods.

Let's scope your project. Send us your collected volume, average basket and platform, and we will calculate the annual saving and the integration cost between EUR 1,000 and 4,000 excl. VAT with a switchover in 2 to 4 weeks. Detailed quote within 48 h. WhatsApp +221 77 596 93 33.