The verdict in three sentences
In Nigeria, Paystack charges 1.5% + NGN 100 locally (capped at NGN 2,000) and 3.9% on international cards, while Flutterwave sits near 1.4% local with T+1 payout. But the headline rate hides the real cost: the fixed fee, the cap and the settlement delay shape your effective rate more than the percentage alone. The right pick depends on your average ticket size, your card-vs-transfer mix and how much you value next-day cash.
The merchant rate is only part of the cost
The true cost of collecting a payment breaks into three layers: the merchant commission (a percentage), an optional fixed fee per transaction, and the cost to settle funds into your bank account. A 1.5% rate with a NGN 100 fixed fee hits small tickets hard, while a flat 1.4% is cleaner on low-value sales.
| Gateway | Merchant rate | Fixed fee | Cap | Settlement delay |
|---|---|---|---|---|
| Paystack (local) | 1.5% | NGN 100 | NGN 2,000 | T+1 |
| Paystack (intl card) | 3.9% | NGN 100 | none | T+1 to T+2 |
| Flutterwave (local) | ~1.4% | none | varies | T+1 |
| Flutterwave (intl) | 3.8% | none | none | T+1 to T+2 |
These are 2026 order-of-magnitude figures: actual rates are negotiated by volume and by the merchant contract signed with the gateway.
What settlement really costs
Moving money from the gateway to your bank adds a timing cost merchants often ignore.
| Gateway | Payout timing | Transfer/withdrawal fee | Minimum threshold | Auto payout |
|---|---|---|---|---|
| Paystack | T+1 | NGN 10-50 transfer | none | Daily |
| Flutterwave | T+1 | NGN 10-45 transfer | none | Daily/weekly |
| Paystack (intl) | T+2 | same | none | Daily |
| Flutterwave (intl) | T+2 | same | none | Weekly |
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Mini case study
Awa runs a cosmetics shop and collects NGN 5,000,000 per month. On Paystack local at 1.5% she pays NGN 75,000 plus fixed fees; the NGN 100 cap keeps small tickets bearable. On Flutterwave at 1.4% flat she would pay NGN 70,000, saving NGN 5,000 a month, or NGN 60,000 a year. Because most of her buyers pay by transfer rather than card, she keeps the lower flat rate as default and routes international cards to whichever gateway quotes the tighter margin.
FAQ
Is Flutterwave always cheaper? On the merchant rate, often yes with its ~1.4% flat local pricing. But if you take many small tickets, Paystack's NGN 2,000 cap can win on large transactions.
Can I run both gateways on one site? Yes. A unified payment module aggregates Paystack and Flutterwave in a single checkout and routes each transaction to the cheaper rail for that payment type.
Is settlement timing negotiable? Partly. High-volume merchants sometimes secure faster payout, but the floor follows the gateway's settlement cycle, typically 24 hours on working days.
Do international card fees hurt margins? Yes, at 3.8-3.9% they roughly triple the local cost. For diaspora buyers, price that into your product or add a small surcharge where allowed.
Let's talk about your project. We integrate Paystack and Flutterwave into one checkout tuned to your real effective fees. 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.
