The Best Online Payment Systems for Small Businesses

As more businesses shift online and with over 2.77 billion people shopping online worldwide, choosing the best online payment system has become essential to running an efficient, customer-friendly operation. From cafés and ecommerce stores to consultants and clinics – small businesses need tools that are fast, secure, and flexible enough to support their day-to-day operations.

In this guide, we’ll look at how online payment systems work and highlight options suited for small businesses, including Noda, a platform that enables instant bank payments and QR code checkouts through open banking.

What is an online payment system?

An online payment system is the technology that allows you to accept payments through your website, booking form, or payment link. It’s what moves the money from your customer’s bank account to yours, securely and efficiently.

In most cases, this involves a few key parts:

• Payment gateway – captures and encrypts your customer’s payment details.
• Payment processor – communicates with the banks to authorise and process the payment.
• Merchant account – temporarily holds the funds before they’re transferred to your main account.

Some systems combine all of these into one platform, while others give you more flexibility to manage each step yourself. Either way, the goal is the same: to get you paid quickly, securely, and with minimal effort.

Types of online payment gateways

There’s no one-size-fits-all approach to online payments. For most small businesses, the right system means choosing a provider that supports the payment methods your customers actually use – like card payments, bank transfers, or digital wallets.

Most small businesses work with a provider that supports one or more of the following payment methods:

Card payments

Card payments are widely used and familiar to most customers. At checkout, they enter their debit or credit card details, and the payment is processed through a provider like Noda, Stripe or PayPal. These platforms handle security, settlement, and compliance for you.

This method is convenient, though fees and settlement times can vary – something to keep in mind when managing cash flow.

Bank-to-bank payments

Also known as account-to-account payments (A2A), these allow customers to pay directly from their bank account – no card required. Common options include:

• Direct Debit – suitable for recurring payments like subscriptions or retainers. Businesses can manage this in-house or use a provider like GoCardless or Mollie.
• Instant Bank Pay – ideal for one-off payments, approved in-app and settled quickly via providers such as Noda.

While A2A payments are increasingly popular, many platforms also support options like Buy Now, Pay Later (BNPL), digital wallets, vouchers, and even crypto, depending on your market and customer base.

Best online payment systems for small businesses

We’ve handpicked five of the most reliable online payment systems for small businesses based on their experience, flexibility, and suitability for everyday business operations:

Noda

Noda is a great fit for small service-based businesses and e-commerce merchants that need a faster, more cost-efficient way to get paid. Powered by Open Banking, Noda lets your customers pay directly from their bank accounts using a secure link or QR code – no cards needed. With lower fees, no chargebacks, and fewer failed transactions, it’s a practical option for businesses that want to keep running costs down.

Noda is ideal for merchants who:

• Offer services, take bookings, or sell goods and digital products online
• Send payment links or request upfront payments
• Work remotely with clients and need secure payment options
• Operate without a traditional website or store

Noda is especially useful for businesses that rely on quick turnaround and want to avoid the delays and costs of traditional payment systems. You’ll get paid instantly, helping you stay on top of day-to-day expenses and cash flow.

It’s also easy to get started. Noda integrates with e-commerce platforms – no developer required. You can accept payments using branded checkout pages, Instant Payment Links, or QR codes, even without a website. This makes it simple to start selling online or take remote payments with minimal setup.

With support for Instant Payment Links, QR codes, and access to local payment rails like Faster Payments in the UK and SEPA in Europe, Noda is a practical choice for merchants working across regions.

Stripe

Stripe is a widely used payment platform for UK and EU businesses that need a reliable way to accept online payments. While it’s known for card processing, it also supports a wide range of global payment methods, including digital wallets and local bank options.

It offers a complete set of tools to manage transactions, subscriptions, and invoicing, making it a strong option for digital-first businesses. Stripe is also known for its flexibility, with features that support everything from simple checkouts to more advanced billing setups.

Stripe is best for:

• E-commerce stores offering online checkouts
• SaaS companies and consultants with recurring billing
• Digital product sellers who need payment flexibility

While Stripe is more technical and may require a bit of setup, it’s packed with features and support, making it ideal for businesses with growing online operations.

Paypal

PayPal is one of the most recognisable names in online payments, with over 434 million active accounts globally as of Q4 2024. For small businesses, it offers a fast and trusted way to start accepting payments without the complicated setup.

Customers can pay using their PayPal balance, linked bank account, or cards, which makes it a convenient option for one-off payments, digital services, and online sales. While it's easy to set up, the range of supported payment methods is more limited compared to some newer platforms.

PayPal is best for merchants who:

• Want a quick, familiar way to accept payments
• Serve international customers or digital-first buyers
• Prefer built-in tools like invoicing, subscriptions, or pay-by-link

While PayPal’s fees can be higher than some newer providers, its global reach, buyer protection, and strong brand recognition make it a popular choice for small businesses looking for credibility and ease of use.

GoCardless

GoCardless is built for small businesses that rely on recurring payments, like subscriptions, retainers, or memberships. It uses Direct Debit to collect payments directly from your customer’s bank account, helping you take control of cash flow and reduce the admin that comes with chasing invoices.

GoCardless is best for merchants who:

• Want to simplify payment collection without high fees
• Offer services on a subscription, invoice, or one-off basis
• Use accounting tools like Xero or QuickBooks

It’s a flexible option for service-based businesses, consultants, and small businesses looking for a more reliable way to get paid, without relying on cards.

Mollie

Mollie is a flexible payment provider that supports various payment methods, including cards, Apple Pay, PayPal, Klarna, and local European options like iDEAL and Bancontact. It’s particularly strong in the EU and is designed to make setup easy, even for non-technical users.

Mollie supports small businesses that:

• Sell across European markets and need local payment options
• Want flexibility without needing a developer
• Run e-commerce or digital service businesses with varying payment needs

You can add Mollie to your checkout using plugins for platforms like WooCommerce, Shopify, or Magento. The interface is clean, and pricing is transparent. It’s a great option for small businesses looking for international reach and a wide choice of payment methods in one place.

How to choose the right online payment system for your small business

The best payment system should support the way you work, not slow you down. Start by identifying what matters most: faster access to funds, lower fees, or a smoother checkout experience. Think about how your customers prefer to pay and choose a system that makes that process quick and intuitive.

It’s also worth comparing how different options handle transaction speed, payment confirmation, and integration with your tools. Some let you accept payments through secure links or QR codes – added to invoices, shared via email or chat, or embedded in your digital checkout.

The easier it is for customers to pay, the more likely they are to complete the transaction and come back again.

Take payments your way with Noda

Take payments your way with Noda. Designed with small businesses in mind, Noda makes it easy to accept online payments without adding more to your to-do list. You can set up branded checkout pages, integrate instant payment buttons, or use secure links and QR codes – whichever works best for your workflow.

Here’s what Noda brings to your business:

• Access to over 2,000 banks across 28 countries, including the UK, Europe, Brazil, and Canada
• Multi-currency support to accept international payments without extra setup
• Accept cards and open banking payments through one platform
• Real-time confirmation so you know when a payment is complete
• Keep more of each payment with fees as low as 0.1% up to to 1%
• A dedicated account manager who understands your business

Thousands of small businesses across the UK and Europe use Noda to manage online payments more efficiently. Find out how it could work for yours.