The verdict in three sentences
In Nigeria in 2026, Paystack charges 1.5 % + 100 NGN per transaction, capped at 2,000 NGN, while Flutterwave sits at 1.4 % with no per-transaction cap on cards. For a store processing 2,000,000 NGN a month, the fee gap can reach 8,000 to 12,000 NGN — margin that quietly disappears. The right pick depends on your average basket, but for African stores the smartest move is often to accept both mobile money and cards through one unified checkout.
Fees, caps and settlement: the 2026 reference table
The figures below are 2026 orders of magnitude for a merchant account, before volume negotiation. They vary with your KYC tier and provider agreement.
| Criterion | Paystack | Flutterwave | Wave (Senegal, ref.) |
|---|---|---|---|
| Local fee | 1.5 % + 100 NGN | 1.4 % | 1 % |
| Per-transaction cap | 2,000 NGN | None (cards) | None |
| International cards | 3.9 % + 100 NGN | 3.8 % | n/a |
| Settlement delay | T+1 | T+1 | Instant |
| Webhook confirmation | Yes | Yes | Yes |
| Payout to bank | Free daily | Free daily | Free |
| QR / in-person | Yes | Yes | Yes |
Real cost for 100 transactions of 20,000 NGN
What matters is total cost on a realistic volume. Here is the bill for 100 sales of 20,000 NGN (2,000,000 NGN revenue) over one month.
| Line item | Paystack | Flutterwave | Gap |
|---|---|---|---|
| Per-tx fee | 400 NGN | 280 NGN | 120 NGN |
| Fee x 100 tx | 40,000 NGN | 28,000 NGN | 12,000 NGN |
| Monthly total | 40,000 NGN | 28,000 NGN | 12,000 NGN |
| Annualized | 480,000 NGN | 336,000 NGN | 144,000 NGN |
| Effective rate | 2.0 % | 1.4 % | +0.6 pt |
Over a year, the wrong setting costs over 140,000 NGN — the price of a product-page redesign or an ad campaign.
Mini case study
Chidi, who runs a cosmetics store in Lagos, processes 3,600,000 NGN a month. Routing everything through Paystack cost roughly 72,000 NGN/month in fees. By moving high-value card sales to Flutterwave (1.4 %, no cap) and keeping Paystack for smaller baskets that benefit from the 2,000 NGN cap, his bill dropped to about 54,000 NGN/month. Savings: 18,000 NGN/month, or 216,000 NGN/year, with no change to his catalogue. The only cost: wiring both providers into one checkout.
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FAQ
Is Flutterwave always cheaper than Paystack?
Not always. Flutterwave's 1.4 % wins on large baskets, but Paystack's 2,000 NGN cap makes it cheaper on transactions above roughly 130,000 NGN. Map your basket distribution before deciding.
Should I offer both providers on my store?
Yes. Routing each transaction to the cheaper processor and giving customers a fallback if one is down reduces cart abandonment and lost sales.
Do caps block a store selling high-ticket items?
Caps affect fees, not sales limits. For high-value goods, the 2,000 NGN Paystack cap is a real advantage — a 500,000 NGN sale costs 2,000 NGN instead of 7,500 NGN at a flat 1.5 %.
Can I negotiate fees with volume?
Beyond roughly 20,000,000 NGN/month, both providers will discuss custom rates. Bring your last three months of statements before negotiating.
Let's talk about your project. We integrate Paystack, Flutterwave and mobile money into a single checkout for your store. 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.
