E-commerce11 min read

Online payment setup for SMEs: fees comparison in 2026

Mohamed Bah·Fondateur, Kolonell
September 2, 2026
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Online payment setup for SMEs: fees comparison in 2026

Online payment setup for SMEs: fees comparison in 2026

E-commerce

The verdict in three sentences

A PSP's headline rate is never the real cost: reconciliation, refunds and non-EU cards make the bill. In 2026, expect 1.3 to 1.8 % + 0.25 EUR per European card transaction, plus internal reconciliation time. The technical integration ships in 2 to 4 weeks; the right choice is made on full TCO, not the front-facing rate.

PSP fee comparison

The three PSPs most used by French SMEs are close on the European card, but diverge on international cards, transfers and side functions.

PSPEU cardNon-EU cardSEPA transferRefund
Stripe1.4 % + 0.25 EUR2.9 % + 0.25 EUR0.80 % (capped)Fixed fee kept
Mollie1.8 % + 0.25 EUR2.9 % + 0.25 EUR0.25 EURFree
Stancer~0.9 % + 0.15 EURVariablePer planFree

Rates are 2026 orders of magnitude, before volume negotiation. Above ~50,000 EUR monthly volume, most PSPs negotiate a 0.1 to 0.4 point discount.

Total cost of ownership (TCO)

The commission rate is only 60 to 75 % of the real cost. Add integration, 3-D Secure security and above all reconciliation time.

Line itemOne-offRecurring
Technical integration3,000-9,000 EUR
3-D Secure / SCA setupIncluded
Commissions (e.g. 40,000 EUR/month)~600-750 EUR/month
Manual reconciliation2-6 h/week
Automated reconciliation2,000-6,000 EUR~0.5 h/week
Disputes / chargebacks15 EUR per dispute

Automating bank reconciliation is often the best-ROI line: it removes several weekly hours of an accounting profile.

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Mini case study

Sophie, CFO of an e-commerce SME in Bordeaux, collects 40,000 EUR a month online. Her Stripe commissions are ~640 EUR/month. But her accounting team spends 5 hours a week reconciling payments, refunds and transfers, i.e. ~20 hours/month at 35 EUR loaded = 700 EUR/month of hidden cost. By automating reconciliation (4,500 EUR project) she cuts that to under one hour a week, saving ~560 EUR per month: the investment is recouped in 8 months.

FAQ

Which PSP to start with? Stripe for technical depth and international, Mollie for simplicity and free refunds, Stancer for an aggressive EU-card rate. It depends on your card mix.

Is 3-D Secure mandatory? Yes, strong authentication (SCA) is required in the EU. It is included in PSPs but can cut conversion by 2 to 5 % if poorly tuned.

What do chargebacks cost? About 15 EUR per dispute at most PSPs, plus the potentially lost amount. Good anti-fraud settings keep them below 0.3 % of transactions.

Can we collect via SEPA transfer? Yes, cheaper than card for large B2B amounts, but with a 1-2 day delay. Useful above a 1,000 EUR basket.

What is the integration timeline? 2 to 4 weeks depending on the platform and the need for automated reconciliation.

Let's scope your project. Specify your monthly volume, card mix and accounting tool: indicative budget 3,000-15,000 EUR integration + reconciliation, deployment 2-4 weeks. Detailed quote within 48 h. WhatsApp +221 77 596 93 33.

Tags:#SME online payment#PSP fees#Stripe Mollie#3D Secure#card payment fees#payment reconciliation
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Mohamed Bah

Fondateur, Kolonell

Passionate about digital and entrepreneurship in Africa, Mohamed has been helping Sénégalese businesses with their digital transformation since 2020. Founder of Kolonell, he believes every SME deserves a professional and accessible online présence.