The verdict in three sentences
Both Nigerian aggregators cover cards, transfers and mobile money, but their grids differ: Paystack charges 1.5% + 100 NGN capped at 2,000 NGN, ideal for high baskets, while Flutterwave runs a flat ~1.4% with no cap, cheaper on small tickets. For comparison, West African franc-zone aggregators (Hub2 1.8-2.2%, CinetPay ~2.5%, PayDunya ~2.9%) cover Wave, Orange Money, MTN and Moov. Choose on three axes: real fees, settlement delay and webhook reliability, not just the headline percentage.
Fees, settlement and coverage (2026)
The gross percentage hides differences in payout timing and technical quality. Here is the 2026 order of magnitude.
| Aggregator | Estimated 2026 fee | Settlement | Rails | Webhook |
|---|---|---|---|---|
| Paystack | 1.5% + 100 NGN (cap 2,000) | T+1 | cards, transfers, USSD | excellent |
| Flutterwave | ~1.4% | T+1 to T+2 | cards, momo, transfers | good |
| Hub2 (WA) | 1.8 to 2.2% | T+1 to T+2 | Wave, OM, MTN, Moov | signed, reliable |
| CinetPay (WA) | ~2.5% | T+2 | Wave, OM, MTN, Moov | robust |
| PayDunya (WA) | ~2.9% | T+2 to T+3 | OM, MTN, Moov | fair |
Paystack's cap makes it predictable on large orders; Flutterwave's pure percentage wins on small ones.
Impact on the margin of an average basket
One fee point is invisible on a single transaction but adds up fast. Here is the effect across monthly sales levels.
| Monthly sales | Fees at 1.4% | Fees at 1.5%+cap | Fees at 2.9% | Gap low vs high |
|---|---|---|---|---|
| 3,000,000 FCFA | 42,000 | ~45,000 | 87,000 | 45,000 FCFA |
| 8,000,000 FCFA | 112,000 | ~120,000 | 232,000 | 120,000 FCFA |
| 15,000,000 FCFA | 210,000 | ~225,000 | 435,000 | 225,000 FCFA |
| 30,000,000 FCFA | 420,000 | ~450,000 | 870,000 | 450,000 FCFA |
On a 15,000 NGN average basket, Paystack's 2,000 NGN cap only bites above ~133,000 NGN per order; below that, Flutterwave's flat rate is marginally cheaper.
Mini case study
Ngozi runs a ready-to-wear store in Lagos doing 15,000,000 FCFA in monthly sales with a high average basket. On a 2.9% grid she would pay 435,000 FCFA in fees. Switching to Paystack with its cap and 1.5% base, she drops to about 225,000 FCFA, saving 210,000 FCFA each month, some 2,520,000 FCFA over the year, without touching conversion. The technical migration took 4 business days. Payback: immediate in the first month.
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FAQ
Which aggregator has the best webhook?
Paystack is the reference for reliability and HMAC signatures. Flutterwave is solid too; the franc-zone options (CinetPay, Hub2) offer robust signed webhooks, while PayDunya needs more handling of delays.
Can you negotiate fees?
Yes. Most aggregators adjust rates above roughly 10,000,000 FCFA of monthly volume. Bring real volumes and a 3-month history to get the best grid.
Is T+3 settlement a problem?
For tight cash flow, yes: three days of blocked sales can mean several million FCFA. Prefer T+1 or T+2 if your working capital is stretched.
Do you need a different aggregator per country?
Not necessarily. Flutterwave and Hub2 span multiple countries; a single multi-country contract simplifies reconciliation.
How much does migrating aggregators cost?
As a 2026 order of magnitude, 3 to 5 dev days to repoint checkout and webhook, roughly 200,000 to 350,000 FCFA, quickly recovered by the fee gap.
Let's talk about your project. We compare your real volumes and wire the aggregator that best protects your margin. 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.
