The verdict in three sentences
Online payment fees are not uniform across African markets: for the same volume, the effective rate changes with the country, the PSP and your basket structure. Paystack sits at 1.5% + NGN 100, Flutterwave around 1.4%, and M-Pesa around 1.5%, but the fixed fees, thresholds and caps reshape the equation for small and large baskets. Picking the right PSP mix per market can cut your payment bill by 20 to 40%.
Fee comparison by provider
2026 order-of-magnitude figures for merchant collection. Real rates depend on contract and negotiated volume.
| Provider | Region | Commission | Fixed fee | Cap / transaction |
|---|---|---|---|---|
| Paystack | Nigeria | 1.5% + NGN 100 | NGN 100 | ~NGN 2,000 |
| Flutterwave | multi | 1.4% | variable | variable |
| M-Pesa | Kenya | 1.5% | tiered | daily cap |
| Wave | WAEMU | 1.0% | FCFA 0 | no low cap |
| Orange Money | Senegal / CI | 1.5% | FCFA 0 | wallet cap |
| Moov Money | CI / Burkina | 1.7% | FCFA 0-50 | wallet cap |
| Free Money | Senegal | 1.4% | FCFA 0 | wallet cap |
The detail that matters: on small baskets, a NGN 100 fixed fee (Paystack) sharply raises the effective rate, whereas a pure-percentage model (Wave) stays neutral at any amount.
How average basket size drives the effective rate
The same provider does not cost the same percentage depending on transaction size. Illustration with a 1.5% + NGN 100 fixed fee.
| Average basket | % fee | Fixed fee | Effective rate |
|---|---|---|---|
| NGN 1,000 | 15 | 100 | 11.5% |
| NGN 5,000 | 75 | 100 | 3.5% |
| NGN 15,000 | 225 | 100 | 2.2% |
| NGN 50,000 | 750 | 100 | 1.7% |
| NGN 150,000 | 2,250 | 100 | 1.57% |
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Clear takeaway: if your average basket is low, avoid fixed fees and favour a pure-percentage provider. If your basket is high, the fixed fee becomes negligible and you can arbitrate on percentage alone.
Mini case study
Chidi sells accessories in Lagos with a NGN 4,000 average basket and 800 transactions a month, i.e. NGN 3,200,000 in volume. With a provider at 1.5% + NGN 100 fixed, he pays roughly NGN 128,000 in monthly fees. By moving to a provider at 1.0% with no fixed fee, his bill falls to NGN 32,000 — a saving of NGN 96,000 a month, nearly NGN 1,150,000 a year, just by changing PSP mix.
FAQ
Is the cheapest PSP always best? On pure percentage, often yes. But availability, customer coverage and payout speed also count: the real winner is the provider your customers actually use while offering a good rate.
Should I offer several payment methods on my site? Yes. Offering card + mobile money covers the vast majority of customers and prevents cart abandonment from a missing method, which can reach 15 to 25%.
Are advertised rates negotiable? Above a meaningful monthly volume (often NGN 5-10 million), most PSPs accept a discount. Document your volume before negotiating.
How do I handle a multi-country catalogue? Use a unified payment layer that routes each transaction to the cheapest provider in the customer's country, with consolidated reporting for your accounting.
Let's talk about your project. We wire up the right Paystack, Flutterwave, M-Pesa and Stripe mix for your basket and target markets. WhatsApp +221 77 596 93 33.
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.