The verdict in three sentences
For a Nigerian store selling mostly to local customers, Paystack offers the smoothest local integration, while Flutterwave wins on multi-country coverage and Stripe matters only if you invoice international card holders. The right choice depends on your monthly volume, your average basket, and how many payment operators your customers actually use. Below 3M NGN of monthly volume, integration simplicity wins; above it, every point of fees saved is worth hundreds of thousands of NGN per year.
Fees, settlement and coverage: the 2026 reference table
Aggregators charge collection as a percentage of the amount received, sometimes with a fixed fee per transaction. Here are 2026 orders of magnitude for local rails.
| Aggregator | Local rail fee | Card fee | Payout | Countries | Setup |
|---|---|---|---|---|---|
| Wave API (direct) | 1.0-1.5 % | not native | T+1 | 2-3 | 0 FCFA |
| PayDunya | 2.5-3.0 % | 3.5 % + 100 FCFA | T+1 to T+2 | 6-8 | 0 FCFA |
| CinetPay | 2.8-3.5 % | 3.5 % | T+2 to T+3 | 12-15 | 0-50,000 FCFA |
| Paystack (NGN) | 1.5 % + 100 NGN | 2.9 % + 100 NGN | T+1 | 4 | 0 FCFA |
| Flutterwave | 1.4-2.8 % | 3.8 % | T+1 to T+3 | 15+ | 0 FCFA |
Local rail fees are the bulk of your real cost: on 2M NGN collected per month, moving from 3.2% to 1.4% saves roughly 36,000 NGN per month, or 432,000 NGN per year.
Service quality and integration
Beyond price, API reliability and operator breadth matter. An aggregator that covers cards, bank transfer and USSD in a single call spares you integrating four separate APIs.
| Criterion | Paystack | Flutterwave | Stripe |
|---|---|---|---|
| Announced API uptime | 99.9 % | 99.7 % | 99.99 % |
| Local methods per call | 4-5 | 8-12 | cards only |
| Signed webhooks | yes | yes | yes |
| Full sandbox | yes | yes | yes |
| Support response | < 24 h | 24-48 h | 24-72 h |
| SDK / plugin | REST + SDK | REST + plugins | rich SDK |
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Mini case study
Chidi, who runs a cosmetics store in Lagos, collects 1,800,000 NGN per month, 70% by bank transfer and 30% by card. With a 3.2% blended provider he pays 57,600 NGN in monthly fees. By routing bank transfers (1,260,000 NGN) through Paystack at 1.5% and keeping cards on the same provider, his bill drops to about 32,300 NGN, saving 25,300 NGN each month (303,600 NGN per year) for one extra day of development.
FAQ
Which aggregator should I pick if I sell only in Nigeria? Paystack for local bank transfer and USSD, adding cards on the same provider. You minimise fees on the dominant channel while keeping full coverage.
Do quoted fees include VAT? Often not: add 7.5% VAT in Nigeria on the aggregator's commission, so a quoted 3.0% becomes roughly 3.22% effective.
How long until I get paid? Expect T+1 with Paystack, T+2 to T+3 with Flutterwave depending on the country and weekends. A shorter delay improves your cash flow.
Can I switch aggregator later? Yes, if your checkout is built on an abstraction layer. Budget 1 to 3 days of integration to add or replace a provider without touching the purchase funnel.
Do I need business registration to open a merchant account? Yes for live mode: CAC registration, a director's ID and sometimes a bank statement. Activation takes 2 to 10 business days.
Let's talk about your project. We integrate the right aggregator for your volume and operators, with reliable webhooks and optimised settlement. 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.
