The Ultimate Guide to Ecommerce Payment Processing

Ecommerce payment processing is the key to a successful online store – the way you turn a potential sale into reality. From ensuring smooth transactions to building customer trust, choosing the right system is critical. This guide covers everything you need to know to choose the right ecommerce payment setup and grow your business.

January 27, 2025
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What is the best ecommerce payment processing?

With everything riding on the last click, you want to make sure your ecommerce payment processing is offering the easiest experience possible. The best payment processors offer seamless integration, competitive fees, and robust security. Industry leaders like Stripe, Shopify Payments, and PayPal dominate the market, each providing unique features:

  • Stripe: Known for its powerful APIs, Stripe allows advanced customisation for businesses handling high transaction volumes.
  • Shopify Payments: Integrates directly with Shopify stores, eliminating the need for third-party gateways and reducing fees.
  • PayPal: Trusted globally, PayPal supports multiple payment methods, including digital wallets and BNPL options like PayPal Credit.

Choosing the right processor starts with understanding your business needs, from transaction volume to integration requirements. For instance, small businesses with limited resources might prioritise simplicity and cost-effectiveness, while larger enterprises may want to go for flexibility and advanced analytics.

How to manage ecommerce transactions with payment processing

Managing transactions requires accuracy and reliability. Keeping on top of your transactions is an essential part of keeping your business on track, ensuring you can effectively track money in and out of your business.

  • Regular reconciliation: Payment reconciliation helps you match sales with processor reports to avoid discrepancies. Automated reconciliation tools, such as QuickBooks, save time and reduce errors, often integrating directly with your processing system.
  • Ensuring compliance: Running an ecommerce store means you're responsible for your customers’ financial data. That means it’s essential to adhere to PCI DSS standards to secure cardholder data and protect your business from potential fines.
  • Tracking settlements: Monitor cash flow to ensure timely payouts. Platforms like GoCardless provide real-time updates on transaction statuses, helping businesses plan their finances effectively.

How to use payment processing for B2B ecommerce sales

B2B ecommerce transactions often involve higher transaction values and require specialised solutions. Key features to look for include:

  • Flexible payment terms: Options like invoice-based payments or iwocaPay, which provides instant credit to buyers while sellers receive payment upfront.
  • Bulk transaction support: Handle large orders efficiently using processors like Stripe, which supports advanced APIs for complex B2B needs.
  • Robust reporting: Tools like NetSuite offer detailed insights into transaction trends and customer behaviour, enabling better decision-making.

By incorporating these solutions, B2B businesses can streamline operations, reduce payment delays, and improve customer relationships.

Is there an ecommerce website builder with payment processing?

Yes! Platforms like Shopify, BigCommerce, and Wix offer built-in payment solutions:

  • Shopify: Shopify Payments integrates seamlessly into stores, offering features like multi-currency support and fraud detection.
  • BigCommerce: Provides flexibility with multiple gateway integrations, including PayPal and Authorize.net, while supporting advanced customisation.
  • Wix: Simplifies payment processing for small businesses with options for recurring billing and alternative payment methods.

These all-in-one platforms simplify integration, reduce technical complexity, and provide tools for managing transactions, analytics, and customer support.

Key elements of payment processing for ecommerce businesses

Payment gateways

Gateways like Stripe and PayPal securely connect your website to payment processors.

  • They verify payment information, authorise transactions, and ensure smooth fund transfers. 
  • Many include extra features to keep your business safe: Stripe supports real-time fraud prevention, while PayPal offers dispute resolution services.

Merchant accounts

Merchant accounts temporarily hold funds before transferring them to your business account. They're essential for processing credit card payments and are often bundled with payment gateways for convenience.

Payment processors

Processors handle the technical work of executing transactions, ensuring funds flow from customer to merchant easily and reliably. It’s worth noting that they’re technically different from payment gateways – gateways help merchants and buyers connect to processors. Examples include Adyen, which supports international payments, and GoCardless, ideal for recurring payments. However, some providers offer both payment processing and payment gateway services as part of an integrated solution, such as Stripe.

Security protocols

Secure payments rely on SSL encryption, tokenisation, and PCI compliance to ensure that customer and business data is not accessible as it moves between systems. For example, Shopify Payments encrypts all transaction data between nodes to ensure no unauthorised access.

Fraud prevention

Tools like 3D Secure and AI-driven monitoring systems reduce fraud risk while maintaining a smooth checkout. The balance is to keep customers safe and secure while not adding too many extra steps. For instance, Stripe Radar analyses millions of data points to detect suspicious transactions, helping it flag behaviour, while other systems might use tools like two-factor authentication (2FA).

UX

UX stands for user experience – the way your customer interacts with your payment processing system. An easy, intuitive payment flow improves conversion rates and reduces drop-offs during checkout. Features like autofill for card details or one-click payments enhance the user experience by saving steps for the customer, which can be delivered by the gateway or even the browser your customer is using.

Mobile optimisation

With 70% of ecommerce sales happening on mobile, responsive design and mobile wallets are must-haves. Apple Pay and Google Pay also simplify payments for mobile users, boosting conversions, so it’s useful to have integrations with these tools.

Integration capabilities

Platforms like Shopify and WooCommerce allow easy integration of payment gateways, reducing development time and cost. For example, WooCommerce supports over 100 payment gateway extensions, giving you more choice over how you sell.

Regulatory compliance

Meeting standards like GDPR and PCI DSS builds trust and avoids legal issues. Compliance tools integrated into platforms like BigCommerce ensure your business remains audit-ready and secure.

Cross-border transactions

With 55% of online shoppers worldwide having purchased from another country in the last 12 months, multi-currency processing and language support can help you reach international customers. Stripe’s multi-currency feature supports over 135 currencies, while PayPal facilitates seamless cross-border payments.

Customer support

Reliable processors offer 24/7 support, ensuring smooth resolution of issues. Shopify and Stripe both provide dedicated support teams to assist merchants.

Close more deals with iwocaPay

Payment processing isn’t just a technical necessity—it’s the safeguard for customer experience and business growth. By choosing the right systems, you can boost conversion rates, ensure compliance, and unlock new markets, especially if you can offer flexible terms. 

The global market for B2B buy-now-pay-later is growing fast, rising 33.4% every year. With iwocaPay, you can offer your customers a range of payment terms while still getting paid upfront. Enhance your checkout experience, secure transactions, and scale your business effortlessly. Start your journey today!

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Henry Bell

Henry is an experienced financial writer with 8+ years of expertise covering the financial industry and small-to-medium enterprises (SMEs).

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