E-commerce Payment Processors

Accept online card payments with checkout, APIs, and fraud tools.

The right e-commerce processor balances transparent per-transaction pricing with the checkout experience, payment methods, and fraud tooling your store needs. Compare online card rates, supported wallets, and platform integrations below.

41 processors

Payroc-owned New Jersey ISO selling a proprietary gateway to B2B and large-ticket merchants. No rates published, and the contract runs three years.

Custom quote

online rate

Custom quote

monthly fee

Varies

payout

B2B Invoicing
Large Ticket Merchants
Level III Processing
+1
Elavon logo
No reviews

U.S. Bank's merchant acquirer, with more than 2 million customers in the US, Europe and Canada and merchant processing in over 30 countries, on quoted pricing.

From 2.90% + $0.30 per qualified transaction

online rate

$10 small business fee, per CardFellow

monthly fee

2-day

payout

Hotels and restaurant groups
Multi-location retail
Airlines and travel
+1
FinCobra logo
No reviews

Non-custodial crypto checkout that settles BTC, USDT and USDC straight to wallets you control, free to $1,000 then a flat 0.5%.

No card payments

online rate

$0, WooCommerce plugin is $99 a year

monthly fee

Instant

payout

Crypto-native SaaS
Direct-to-wallet settlement
Stablecoin invoicing
+1
Billsby logo
No reviews

UK subscription billing platform that charged a base monthly fee plus a small percentage of billed revenue above a free allowance.

Set by your gateway

online rate

$35 to $45 reported

monthly fee

Varies

payout

Small Subscription Businesses
Hosted Checkout
Low Monthly Billings
Lemon Squeezy logo
No reviews

Merchant of record for digital products at 5% + 50 cents a sale, owned by Stripe since 2024 and now steering sellers to Stripe Managed Payments.

5% + $0.50

online rate

None

monthly fee

Varies

payout

Indie software sellers
SaaS with global VAT exposure
License key delivery
+1

Ecommerce Payment Processing Buyers Guide

Updated August 2026

For online stores the processor is part of the checkout experience, not just a back-office cost. This guide covers the APIs, fraud tools, and conversion features that separate ecommerce-first providers from general processors.

Key takeaways

  • Checkout UX and hosted-page quality directly affect conversion.
  • Built-in fraud tooling reduces chargebacks without blocking good customers.
  • Native platform integrations (Shopify, WooCommerce) cut integration time.

What is ecommerce payment processing?

Ecommerce payment processing handles card and wallet payments made on your website or app. Beyond moving the money, an ecommerce processor provides the checkout components (hosted pages, embeddable fields, or full APIs) plus the fraud and tokenization tools online sales depend on.

What are the benefits for an online store?

  • Optimized checkout that reduces cart abandonment.
  • Support for wallets like Apple Pay and Google Pay out of the box.
  • Tokenized card storage for subscriptions and one-click reorders.
  • Fraud scoring that adapts to your order patterns.

What to consider before buying

Weigh the integration effort against your platform: a native Shopify or WooCommerce plugin can save weeks versus a raw API. Confirm the fraud tools, chargeback handling, and whether recurring billing is supported natively if you sell subscriptions.

Frequently asked questions

What do ecommerce payment processing companies charge for online sales?
Online transactions typically run 2.6% to 3.5% depending on the provider, with some offering lower rates for higher monthly volume.
What's the difference between digital payment processing companies and in-person processors?
Digital-first processors focus on checkout APIs, hosted pages, and fraud tools for online sales, while in-person processors are built around card readers and POS hardware.
Which ecommerce payment processing companies integrate with Shopify?
Several processors on this list offer native Shopify integrations; filter by the Shopify integration tag to see them side by side.