Top 10 Payment Gateways for Nigerian Ecommerce Websites

Running an ecommerce business in Nigeria means dealing with one key challenge — seamless online payments. A great product and a functional website mean little if customers can’t pay easily or securely. For business decision-makers, choosing the right payment gateway in Nigeria goes beyond checkout buttons; it affects conversion rates, customer trust, and long-term scalability.

Below is a practical breakdown of the 10 best payment gateways for Nigerian ecommerce websites, tailored to help founders, operations managers, and IT leads make informed decisions.

1. Paystack: The Pioneer of Modern Payments in Nigeria

Overview:
Paystack remains a leading choice among Nigerian startups and SMEs. Acquired by Stripe in 2020, it offers a robust API, simple dashboard, and transparent pricing.

Key Features:

• Supports Visa, Mastercard, Verve, and bank transfers

• Instant settlements to local bank accounts

• Recurring billing and subscription support

• Fraud detection and chargeback management

Pricing:
1.5% + ₦100 per local transaction (₦100 waived for transactions under ₦2,500).
3.9% per international transaction.

Ideal For:
Ecommerce stores, SaaS platforms, and service-based businesses that need developer-friendly integration.

2. Flutterwave: Africa’s Payment Infrastructure Giant

Overview:
Flutterwave is known for powering payments across Africa and beyond, trusted by brands like Uber and Binance. It enables businesses to accept payments in multiple currencies through cards, bank transfers, and mobile money.

Key Features:

• Global reach across 30+ countries

• Accepts cards, bank transfers, and Barter payments

• Simple checkout integration for WooCommerce and Shopify

• Excellent reporting and analytics tools

Pricing:
1.4% per local transaction, 3.8% per international payment.

Ideal For:
Enterprises and cross-border ecommerce stores targeting multiple African markets.

3. Moniepoint: Banking Meets Payments

Overview:
Moniepoint (formerly TeamApt) is now a full-fledged business banking and payment service. Its unified dashboard allows merchants to collect, manage, and track payments seamlessly.

Key Features:

• Integrated POS and online payment tools

• Business current account with instant settlement

• Bulk transfers and employee management tools

• 24/7 local support

Ideal For:
Brick-and-mortar retailers expanding into ecommerce, logistics firms, and service providers managing multiple transactions daily.

4. Interswitch WebPay: The Legacy Powerhouse

Overview:
Before the fintech boom, Interswitch WebPay dominated Nigeria’s online payments landscape. It remains a solid choice for established enterprises that value stability and local support.

Key Features:

• Deep bank integrations

• Supports Verve, Visa, and Mastercard

• Strong backend security and fraud controls

Pricing:
Custom pricing based on volume and sector.

Ideal For:
Large corporations, government agencies, and enterprise-level ecommerce platforms.

5. Opay Checkout: Fintech for the Everyday Shopper

Overview:
With millions of wallet users across Nigeria, OPay’s payment gateway gives businesses direct access to its massive user base.

Key Features:

• Direct wallet-to-merchant payments

• Instant settlement to OPay accounts

• Integration with mobile POS and QR code systems

• Competitive transaction fees

Ideal For:
SMEs and ecommerce brands targeting mobile-savvy consumers.

6. Remita: Government-Grade Payment System

Overview:
Remita is widely used for federal and state government payments, but its ecommerce features are equally strong. It supports payments via cards, bank accounts, and mobile wallets.

Key Features:

• Multi-channel payment support

• Trusted by Nigerian public institutions

• Advanced reconciliation tools

Ideal For:
Educational institutions, NGOs, and businesses handling high-volume payments with complex reconciliation needs.

7. Squad by GTCO: Banking Innovation for Digital Businesses

Overview:
Squad, powered by GTCO (GTBank), combines financial credibility with fintech innovation. It provides plug-and-play payment tools for SMEs and large enterprises alike.

Key Features:

• Multiple integration options (API, plugins, payment links)

• Local and international card support

• Settlement within 24 hours

• Intuitive dashboard for analytics

Pricing:
1.5% + ₦25 for local transactions. 3.5% for international.

Ideal For:
Tech-enabled businesses that prefer working within a trusted banking ecosystem.

8. Korapay: Simplifying Cross-Border Payments

Overview:
Korapay is a newer entrant but growing fast across Nigeria and Kenya. It’s built for businesses that need reliable cross-border payment gateways in Nigeria.

Key Features:

• Global virtual accounts (USD, GBP, NGN)

• Supports digital invoicing

• Developer-first integration tools

• Strong anti-fraud systems

Ideal For:
Startups and exporters dealing with clients outside Nigeria.

9. PayU Nigeria: Enterprise-Level Global Gateway

Overview:
PayU operates globally, serving enterprise clients and high-volume ecommerce sites. Its Nigerian arm connects local payment options with global merchants.

Key Features:

• Accepts over 250 local and international payment methods

• Fraud detection powered by AI

• Recurring billing for subscriptions

Ideal For:
Large ecommerce platforms, airlines, and multinational corporations.

10. VoguePay: Affordable Gateway for SMEs

Overview:
VoguePay offers flexible integration and low setup costs, making it attractive for small businesses and freelancers.

Key Features:

• Accepts local and international cards

• Wallet-to-wallet transfer system

• Multi-currency support

Pricing:
1.5% per local transaction, 3.8% for international.

Ideal For:
Microbusinesses and online service providers seeking affordability and simplicity.

Quick Comparison Table: Payment Gateways in Nigeria

What to Consider When Choosing a Payment Gateway

Choosing the right payment gateway in Nigeria depends on your business model, transaction volume, and customer base. Every decision-maker from CEOs to IT leads, should evaluate the following critical factors before committing to a provider:

1. Transaction Fees:
   Even a small difference in transaction fees can significantly impact your bottom line over time. Compare both local and international charges, including hidden fees for chargebacks or currency conversions. For high-volume merchants, consider gateways that offer tiered or negotiated rates to lower costs as your transaction volume grows.

2. Integration Options:
   Compatibility with your existing ecommerce platform is crucial. Before choosing, confirm that the gateway supports WooCommerce, Shopify, Magento, OpenCart, or custom-built platforms. Also, check for available plugins, APIs, or SDKs that simplify setup and allow your development team to integrate quickly without disrupting your site’s performance.

3. Customer Experience:
   Payment friction can lead to cart abandonment and lost sales. Look for gateways that provide a fast, mobile-friendly checkout process, accept multiple payment methods (cards, transfers, USSD, wallets), and automatically detect the best payment option for each user. The more seamless the checkout, the higher your conversion rate.

4. Security and Compliance:
   Online payments demand strict protection of customer data. Prioritize gateways that are PCI-DSS certified and offer features like two-factor authentication, encryption, and fraud monitoring. Compliance with Nigerian regulations and Central Bank of Nigeria (CBN) standards ensures reliability and legal protection for your business.

5. Settlement Speed:
   Timely settlements improve cash flow and daily operations. Choose a gateway that offers same-day or next-day settlements directly to your business account. For high-turnover industries like retail and logistics, this can make a huge difference in maintaining liquidity and meeting supplier payments on time.

6. Customer Support and Reliability:
   Downtime during checkout can cost revenue and credibility. Verify that the payment provider offers 24/7 support, a dedicated account manager, or local service teams in Nigeria. This ensures that any transaction issue or downtime is resolved quickly.

7. Scalability and Global Reach:
   As your business expands, your payment gateway should grow with you. Opt for providers that support multi-currency payments, cross-border transactions, and international cards. Platforms like Flutterwave and Paystack, for instance, offer regional expansion tools that make scaling across Africa simpler.

Trends Shaping Nigeria’s Payment Landscape

The Nigerian fintech ecosystem is evolving rapidly, driven by regulatory reforms and rising ecommerce adoption.
Key trends include:

• Mobile-first transactions: With over 220 million mobile connections, gateways like OPay and PalmPay leverage wallet-based payments for convenience.

• Cross-border ecommerce growth: Startups are using Korapay and Flutterwave to receive USD and GBP payments.

• Embedded finance: Banks like GTCO are building fintech products (Squad) that blend traditional banking and modern APIs.

For decision-makers, these shifts mean more flexibility and competition, and ultimately, better options for both businesses and customers.

Choosing the Right Partner

The best payment gateway in Nigeria is one that aligns with your business model, scale, and growth goals. Whether you’re managing a national ecommerce store or expanding across Africa, the right gateway ensures smooth transactions, improved customer trust, and faster settlements.

eBrand Promotion helps businesses design and deploy ecommerce websites with secure, fully integrated payment gateways tailored to their industry and target market.

Contact eBrand Promotion today to discuss your ecommerce payment integration or digital transformation project.