If you're running an online store using WooCommerce, one of the most important decisions you'll make is choosing how to accept payments. WooCommerce supports popular payment gateways like PayPal and Stripe, but in many cases, store owners need more flexibility. This is where WooCommerce custom payment gateways come in.

Whether you're targeting a specific country, selling niche products, or looking to reduce transaction fees, using a custom WooCommerce payment gateway can give you full control over your checkout experience.

In this post, we’ll highlight the top 7 custom payment gateways for WooCommerce users that offer flexibility, regional support, and advanced features for serious eCommerce growth.

1. Razorpay

Best For: Indian businesses looking for fast, secure, and local payment options.

Why It’s a Great Custom Option:
Razorpay offers a tailored payment gateway plugin for WooCommerce that supports all major Indian payment methods, including UPI, net banking, credit/debit cards, and wallets. What makes it customer-friendly is the wide developer support, easy integration, and the ability to personalize checkout pages.

Key Features:

• Native WooCommerce plugin

• Supports recurring payments

• Smart routing for better payment success

• Custom checkout UI

• Secure with PCI DSS compliance

Bonus: Razorpay supports instant refunds and real-time settlements.

2. Paystack

Best For: WooCommerce stores targeting customers in Nigeria, Ghana, and other parts of Africa.

Why It’s a Great Custom Option:
Paystack is designed for African businesses and has become a trusted brand in the region. It provides a simple, secure checkout process and offers APIs that developers can use to build advanced customizations.

Key Features:

• Accepts card, bank transfers, and mobile money

• Pre-built plugin for WooCommerce

• Detailed transaction reporting

• Seamless checkout with branded UI

• Great for digital and physical products

Bonus: Offers split payments and real-time data insights.

3. Authorize.Net

Best For: U.S.-based businesses looking for robust features and flexibility.

Why It’s a Great Custom Option:
Authorize.Net is a trusted payment gateway that supports custom integrations through its APIs and SDKs. With WooCommerce, it allows advanced controls like stored customer profiles, fraud detection tools, and recurring billing.

Key Features:

• PCI-compliant checkout

• Easy WooCommerce integration via plugin

• Recurring/subscription billing

• Detailed customization options

• Reliable customer support

Bonus: Works with WooCommerce Subscriptions and Memberships plugins.

4. Mollie

Best For: European WooCommerce users looking to offer a variety of local payment methods.

Why It’s a Great Custom Option:
Mollie is known for supporting an impressive number of European payment options, including iDEAL, SEPA, Bancontact, and Klarna. Their WooCommerce plugin offers flexibility for developers and businesses looking for a tailored experience.

Key Features:

• Supports over 20 payment methods

• Multilingual and multi-currency

• Hosted and embedded payment options

• Clear, developer-friendly API

• No setup or subscription fees

Bonus: Ideal for cross-border European commerce.

5. Cryptocurrency Gateways (CoinPayments / NOWPayments)

Best For: Stores that want to accept crypto payments.

Why It’s a Great Custom Option:
With crypto gaining popularity, WooCommerce stores can use gateways like CoinPayments or NOWPayments to accept Bitcoin, Ethereum, and many altcoins. These plugins are highly customizable and allow you to control fees, conversion rates, and supported coins.

Key Features:

• Accept 100+ cryptocurrencies

• Instant payment confirmations

• Supports WooCommerce’s latest versions

• Low transaction fees

• API for advanced crypto integrations

Bonus: Adds a modern edge to your store for tech-savvy customers.

6. Custom Bank Transfer Plugin (Manual Payment Gateway)

Best For: Stores requiring offline payments or regional bank transfers.

Why It’s a Great Custom Option:
Not all businesses want or need an automatic gateway. For example, B2B wholesalers, agencies, or services that rely on invoicing can create a custom bank transfer gateway using WooCommerce's built-in "Direct Bank Transfer" method—enhanced with developer customization.

Key Features:

• Fully customizable with code

• Supports conditional logic (e.g., minimum order amount)

• You can add multiple banks or currencies

• Works well for large transactions

• Zero transaction fees

Bonus: Can be combined with email automation to confirm payment and deliver goods/services.

Custom-Built API Gateway (via WooCommerce Gateway API)

Best For: Enterprises or businesses with proprietary payment systems.

Why It’s a Great Custom Option:
Some companies have their own banking or payment infrastructure. WooCommerce allows you to build a custom payment gateway from scratch using the WooCommerce Payment Gateway API, giving you complete control over security, branding, and processing.

Key Features:

• Fully tailored experience

• Secure server-to-server communication

• Works with any payment processor that offers an API

• PCI-compliant with proper development

• Scalable for large-volume stores

Bonus: This is ideal for businesses with in-house developers or access to WooCommerce development services.

Choosing the Right Custom Payment Gateway

When selecting the best option for your WooCommerce store, ask yourself:

• Where are my customers located?

• What payment methods do they prefer?

• Do I need full control over checkout customization?

• Am I looking to reduce fees?

• Is developer support available for setup?

Each business is unique, and your payment gateway should align with your operational needs, technical capacity, and customer expectations.

Need a Custom Payment Gateway Built?

If none of the ready-made options fit your business model, you can always hire WooCommerce developers to build a completely custom gateway from scratch. This can include:

• Local bank integrations

• Industry-specific regulations

• Custom checkout flows

• Multi-currency support

• Custom fraud checks or 2FA

Make sure to work with experienced developers who understand WooCommerce’s framework and PCI compliance standards.

Final Thoughts

The payment gateway you choose directly affects customer trust, conversion rates, and business operations. Whether you opt for a localized solution like Razorpay, go crypto with CoinPayments, or build your own with WooCommerce’s APIs, the goal is to make checkout simple, secure, and aligned with your brand.

Partnering with a reliable WooCommerce Development Company can help you implement the right payment solution tailored to your specific needs, ensuring seamless integration, security compliance, and long-term scalability.

WooCommerce gives you the flexibility to customize nearly every aspect of your store—including payments. With the right custom gateway, you’re not just collecting money—you’re creating a seamless, scalable customer experience.