Ecommerce payment processing: everything you need to know to get paid online

What is ecommerce payment processing? Read this full guide to find out.

Ecommerce payment processing is the system that securely moves money from your customer's account to yours when they buy online.

Essentially, payment processing handles everything from card authorization to fraud detection to final settlement.

But here's the thing: selling online isn't just about having a great product or offer, it's about making sure people can actually pay you without friction.

Clunky checkout or sketchy payment flows kill trust instantly, and customers bounce before you ever see their money.

Below, we'll walk through how ecommerce payments work, the top payment providers, and how to choose the best provider for your business.

Quick look: 5 popular ecommerce payment providers

Here's a snapshot of 5 of the most popular payment providers for online business:

How ecommerce payments really work

Online payments might feel instant, but there’s a lot happening behind the scenes to make them safe and seamless.

Modern ecommerce runs on two key players: payment gateways (the checkout page your customer sees) and payment processors (the engine that actually moves the money).

Here’s how it flows:

1. A customer enters their payment info through the gateway.
2. The processor verifies the funds and approves the transaction.
3. The money lands in your merchant account after a short payout window.

This whole process is secured by TLS (Transport Layer Security): a protocol that encrypts sensitive data. It’s what turned “typing your card number on a website” from risky to routine.

With ecommerce projected to grow another 7.8% in 2025, speed, security, and reliability aren’t nice-to-haves — they’re the difference between abandoned carts and consistent revenue.

Top 10 ecommerce payment providers compared

1. Whop Payments

Whop is a fully independent payments platform built for modern business.

Our multi-PSP orchestration routes each checkout to the provider most likely to accept it (and retries smartly), lifting successful charges by 6–11% based on configuration.

Whop powers payments for 27,000+ businesses and gives you true global reach: 195 countries, 135+ currencies, and 100+ payment methods, including local wallets, BNPL, and crypto.

Plus, pricing is a flat 2.7% + $0.30 for domestic cards (+1.5% for international, +1% if currency conversion is required).

“Through thousands of conversations, we’ve learned our customers really only care about two things: getting paid and paying out. Our mission is to be the best in the world at solving those problems.”

- Hunter Dickinson, Head of Partnerships at Whop

Payouts are just as flexible. Choose instant or scheduled payouts via ACH, wires, Venmo, invoices, crypto, and more, with global coverage across 200–240+ territories.

You'll also get automated tax calculation and remittance as we act as your Merchant of Record (MoR) for sales tax, VAT, and GST.

Oh, and when you need help? You'll reach 24/7 human support with near-instant response times – plus free account management for higher-volume sellers.

Key takeaways:

• Price: Free to start; 2.7% + $0.30 per successful domestic card charge (enterprise rates available at $50K+ monthly)
• Pros: Global reach (195/135+/100+), orchestration uplift, MoR tax handling, BNPL + crypto, rich product gating, 24/7 human support
• Cons: Best fit for digital-first and hybrid businesses; not a full warehousing/logistics suite for large physical catalogs

2. Stripe

Stripe is a developer-first payments platform with modern APIs, no-code tools, and global coverage. It supports cards, wallets, bank debits/transfers, and BNPL, and bundles strong subscription and invoicing features—great for startups through to enterprises. Standard US online card pricing is 2.9% + 30¢ per successful charge (other methods vary).

Stripe also offers add-ons like Billing, Tax, and Adaptive Acceptance; these can improve revenue and compliance but may add extra cost depending on plan and region.

Stripe key takeaways:

• Price: US online cards typically 2.9% + 30¢; other methods/regions vary. Custom pricing available for large volumes.
• Pros: Excellent APIs and docs, broad global methods, robust subscriptions/invoicing, fast setup
• Cons: Add-ons (Tax, Billing tiers, etc.) can raise total cost; MoR/tax remittance not included by default

3. Paypal

PayPal brings a huge consumer wallet and one-tap checkout that many buyers recognize and trust—plus support for Venmo and standard card processing via PayPal Checkout.

Current US commercial pricing lists PayPal Checkout at 3.49% + a fixed fee (USD fixed fee is $0.49) and standard credit/debit card payments at 2.99% + a fixed fee; international adds +1.5%. Details vary by product.

Do note: PayPal may place holds or reserves on merchant funds in certain risk scenarios (new sellers, high disputes, industry risk, etc.). That's good for buyer protection, but can be frustrating for cash flow.

PayPal key takeaways:

• Price: Typical US rates include 3.49% + $0.49 for PayPal wallet/Checkout and 2.99% + $0.49 for standard card payments; plus +1.5% on international
• Pros: Enormous wallet adoption, fast checkout, flexible options (PayPal, Venmo, cards)
• Cons: Possible account holds/reserves; fee tables can be complex across products

4. Braintree

Braintree (a PayPal company) is a full-stack payments platform and gateway built for web and mobile.

With a single integration, you can accept major cards plus PayPal, Venmo (US), Apple Pay, Google Pay, and selected local methods.

Braintree also supports split payouts via its Marketplace program, but it requires specific approval under a Marketplace Service Provider agreement. This keeps the feature set powerful while adding the compliance guardrails marketplaces need.

Pricing is method-specific and varies by region, risk profile, and product (cards vs. wallets vs. local methods).

PayPal publishes Braintree's fees and notes that they can differ by merchant; confirm your exact schedule on the fees page or with sales.

Braintree key features:

• Price: method-specific; see PayPal's Braintree fee tables for your region and products
• Pros: native PayPal/Venmo/wallet support, marketplace split payouts (with approval), strong PCI posture (Level 1), global reach with multi-currency
• Cons: marketplace requires approval; fee structure can be complex across methods/regions; PayPal ecosystem policies (e.g., reserves/holds) may apply depending on risk profile

5. Apple Pay

Apple Pay is Apple's tokenized wallet built into iPhone, iPad, Apple Watch, and Mac, enabling fast checkout online and in stores with Face ID/Touch ID. It's now available in 78+ markets, supported by 11,000+ bank and network partners, and used at checkout on millions of websites/apps and in tens of millions of stores worldwide. Merchants typically enable it through their processor (e.g., Stripe, Braintree, Adyen).

There's no extra Apple Pay fee to the merchant beyond your normal card processing rates; processors price Apple Pay the same as card-present/online card transactions in your setup. On iOS 18 and later in the U.S., Apple Pay also supports pay-over-time via an integration with Affirm after Apple discontinued Apple Pay Later, giving shoppers BNPL options right inside Apple Pay.

If you sell in person, you can accept contactless payments on an iPhone with Tap to Pay on iPhone—no extra hardware required—so customers can tap a card, Apple Pay, or other wallets directly on your device.

Apple Cash (the peer-to-peer balance used in Apple Pay) is U.S.-only and issued by Green Dot Bank; it powers features like Tap to Cash (NFC P2P by holding two iPhones together). That's separate from Apple Pay itself, which is the wallet used globally for merchant payments.

Apple Pay key takeaways:

• Price: no separate Apple fee; you pay your processor's standard card/wallet rates
• Pros: faster mobile checkout, biometric authentication, network tokenization (card numbers aren't shared with the merchant), broad global availability, optional BNPL via Affirm (U.S.)
• Cons: limited for non-Apple users; Apple Cash P2P is U.S.-only

6. Google Pay

Google Pay is Google's digital wallet for Android and Chrome users. It lets customers store cards, passes, and loyalty points, and pay online or in-store with a tap. In many markets, Google Wallet stores the payment methods, while Google Pay handles the actual transactions.

Transactions are secured with device-level authentication—PIN, password, or biometrics like fingerprint or face unlock—so checkout feels seamless but still safe. It also supports peer-to-peer payments in certain regions, though its primary strength is ecommerce and mobile commerce.

Adoption is climbing steadily, with more ecommerce stores adding it alongside Apple Pay to capture mobile-first buyers.

Google Pay key takeaways:

• Price: No separate Google fee; you pay your payment processor's wallet/card rates
• Pros: Built-in for Android users, fast tap-to-pay online and in-store, strong device security, loyalty integrations
• Cons: Limited to Android/Chrome ecosystem; availability and feature set vary by country

7. Amazon Pay

Amazon Pay leverages Amazon's massive customer base, letting shoppers use their stored Amazon credentials to check out on third-party sites. That means fewer abandoned carts, especially for Amazon-heavy users who trust the brand.

It supports one-time and recurring payments, integrates easily with ecommerce platforms, and offers Amazon's familiar interface at checkout. Merchants benefit from both trust and speed—customers don't need to create a new account or re-enter card details.

Availability is region-based, offered in countries including the US, UK, Germany, Japan, and India. Adoption is growing, but it's not as universal as wallets like PayPal or Apple Pay.

Amazon Pay key takeaways:

• Price: Processor-dependent; generally aligned with card transaction fees (check your provider).
• Pros: Huge consumer trust, frictionless checkout for Amazon account holders, recurring payments support.
• Cons: Limited to supported regions; not as flexible for merchants outside Amazon's ecosystem.

8. Square

Square (a Block, Inc. brand) started as a simple card reader but now powers millions of businesses with POS hardware, online stores, invoices, and APIs. It's especially strong for sellers who operate both in-person and online.

Square has transparent pricing: in the US, 2.6% + 10¢ per in-person tap, dip, or swipe, and 2.9% + 30¢ for online transactions. It also supports cards, wallets (Apple Pay, Google Pay), ACH bank transfers, and gift cards.

Since acquiring Afterpay, Square lets merchants offer BNPL both online and in-person. Customers pay in installments while sellers get paid upfront (minus the Afterpay fee).

Square key takeaways:

• Price: US in-person 2.6% + 10¢; online 2.9% + 30¢. Custom enterprise rates available.
• Pros: Best-in-class POS hardware, strong online store tools, built-in BNPL via Afterpay, easy for hybrid businesses.
• Cons: Primarily US-focused; less global reach and fewer currencies than Stripe or Whop.

9. Klarna

Klarna is one of the biggest names in buy now, pay later (BNPL). Its core offerings: Pay Now, Pay in 30 Days, Pay in 3 or 4 Installments, and financing for larger purchases. These options can boost conversion rates and average order value for merchants.

Klarna integrates easily with major processors like Stripe (via Checkout or Connect), though it uses a redirect flow—shoppers complete payment on Klarna's page before returning to your site. That extra step can impact conversion, but many customers already know and trust Klarna.

It's available in 45+ markets and claims hundreds of millions of active users globally, making it a strong option if your buyers expect BNPL.

Klarna key takeaways:

• Price: Varies by region and product; typically a per-transaction fee plus a fixed charge.
• Pros: Familiar BNPL brand, boosts order value, broad market coverage, Stripe/Braintree integrations.
• Cons: Redirect checkout flow adds friction; fees vary; not all buyers want installment payments.

10. Ayden

Adyen is an enterprise-grade payments platform that handles everything from authorization to settlement in-house.

It’s the backbone for major global brands like Uber, Spotify, and H&M – known for reliability, scale, and cross-border support.

Unlike most gateways, Adyen offers a unified system for online, in-person, and mobile payments, plus deep integrations for marketplaces and platforms.

Its single global platform eliminates the need for multiple PSPs, simplifying compliance and reporting across currencies and regions.

Ayden key takeaways:

• Price: Card fees start around interchange + 0.6% + $0.12 per transaction – no monthly fees, though a $120 minimum monthly invoice may apply depending on volume.
• Pros: Global reach, many supported payment methods, flexible APIs.
• Cons: More complex setup for small businesses; higher minimums make it less friendly for early-stage sellers.

What makes a good ecommerce payment solution?

The best payment providers help directly increase your revenue, customer trust, and long-term growth. Here’s what to look for:

Trust

A good provider gives both you and your buyers peace of mind.

When customers type their card number or connect a wallet, they’re putting faith in you and your payment provider. Most shoppers don’t understand the tech behind TLS, PCI compliance, or tokenization—what they do trust are familiar names and seamless checkout flows.

Security

Security isn’t optional—it’s the backbone of ecommerce.

Any provider worth using should be PCI DSS compliant, use strong TLS encryption, and support tokenization so sensitive details (like card numbers) are never stored in plain text.

Modern providers add fraud detection and risk scoring on top, protecting you from chargebacks and your customers from fraud.

Ability to handle complexity

Only robust platforms can manage all moving parts without downtime, failed payments, or fraud slipping through.

An online transaction isn’t just “customer clicks, you get paid.” Behind the scenes, processors talk to card networks, issuing banks, acquiring banks, and your merchant account (all in real time). Great providers innovate constantly to stay ahead of hackers and evolving payment tech.

Fair, transparent fees

Payment processors make money through transaction fees. Most charge 2.7–3.5% + a small flat fee per transaction, with possible discounts at higher volumes.

What matters is clarity: no hidden surcharges, and flexible pricing if you’re scaling fast.

Support for multiple payment methods

The best providers give you broad coverage: global cards, digital wallets, local methods, BNPL, and even crypto if your audience expects it.

Customers are loyal to their preferred payment method, and if they don’t see it at checkout, there’s a good chance they’ll abandon the cart.

How ecommerce payment solutions impact your business

Choosing the right payment solution directly impacts your sales, your customers’ trust, and even your ability to grow. Here are the key areas where payments make a difference:

Conversion rate

Conversion rate is one of the most important metrics in any online business. A checkout that’s fast, secure, and frictionless will close more sales, while slow or clunky payment flows cause drop-offs.

The variety of payment methods you offer also matters—if shoppers don’t see their preferred option, many will simply abandon the cart.

Customer satisfaction and user experience

The checkout experience shapes how customers feel about your brand. A smooth, familiar payment flow builds confidence and makes people want to come back. On the flip side, confusing or sketchy-looking payment steps create doubt. Customers should feel secure, in control, and reassured by the payment options you provide.

Payout access and management

The best payment providers give you a clear dashboard showing pending and completed payouts, flexible schedules, and options for faster access to cash.

Getting paid in the right currency, without surprise holds or restrictions, makes it easier to manage cash flow and reinvest in growth.

Whop: the smarter way to get paid online

Smooth payments are the difference between customers checking out or bouncing, between cash flow stress and predictable growth.

Where most payment processors stop at moving money from A to B, Whop goes further – and charges you less to do it:

• Global reach without the hassle: Accept 100+ payment methods in 195+ countries, including cards, wallets, BNPL, and crypto—so your customers can pay however they want.
• Built-in growth levers: Unlike Stripe or PayPal, Whop isn’t just infrastructure. It’s also a marketplace where millions of buyers are already browsing offers like yours. That means discoverability is baked in.
• Merchant of record protection: We handle sales tax, VAT, and compliance for you, so you can scale globally without legal headaches.
• Real support, 24/7: Reach an actual human in minutes, not days, whenever you need help.

Power your sales with Whop Payments: no middlemen, no friction, more profit.

Ecommerce payment FAQs

How does payment processing work with ecommerce?

When a customer checks out, their payment details are encrypted and sent through a payment gateway. A processor then talks to the card network, the customer’s bank (issuer), and your bank (acquirer) to authorize the charge and move the money.

How are ecommerce payments made secure?

Modern payment solutions use TLS encryption (the successor to SSL) to secure data in transit, and PCI DSS compliance to keep card details safe. On top of that, most platforms now use tokenization—replacing sensitive data like card numbers with non-sensitive tokens—so the raw details are never stored on your systems.

What is the difference between a payment gateway and a payment processor?

Think of the gateway as the customer-facing part (checkout page, Apple Pay button, PayPal pop-up). The processor is the behind-the-scenes engine that authorizes the charge, verifies funds, and moves money between banks. They work together, but they do different jobs.

Do I need a payment processor for my ecommerce store?

Yes. Every online store needs a processor to handle the movement of funds securely between customers and merchants. Many platforms (like Whop, Stripe, or Braintree) bundle the gateway and processor into one so you don’t have to set them up separately.

What are transaction fees?

Every processor charges per transaction, usually as a percentage of the sale plus a flat fee. In the US, standard card rates are around 2.7–3.5% + $0.30. Rates can vary by payment method, country, and volume—some platforms offer discounts at higher processing levels.

Does a payment processor or gateway collect taxes?

In most cases, no—you as the merchant are responsible for collecting and remitting taxes like VAT, GST, or sales tax. The exception is when you use a provider that acts as Merchant of Record. For example, with Whop Payments, Whop is the Merchant of Record, so taxes, compliance, and remittance are handled automatically.