TL;DR

For most WooCommerce stores, WooPayments or the official Stripe plugin is the best starting point, since both run at 2.9% + $0.30 on US cards with no setup or monthly fees. Add PayPal for consumer recognition and international reach, and choose Easy Pay Direct if you’re in a high-risk category or have been declined or frozen elsewhere. Unlike Shopify, WooCommerce adds no platform fee on any gateway, and you can run several processors at once.

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Most “best payment processor” lists settle on a winner and move on. That’s not much help when the right answer depends on your risk category, your customers’ countries, how fast you need to get paid, and what the real total cost looks like once you add international fees and disputes.

This guide compares four options we’ve researched in depth on the things that actually differ. We’re not covering Square, Authorize.net, Adyen, Braintree, or Worldpay here, because each deserves the same depth rather than a passing mention.

Which Processor Fits Your WooCommerce Store?

Start with your situation, then read the details below:

So what does this mean in practice? Most stores don’t need to choose just one. A common setup is WooPayments or Stripe as your main processor, PayPal alongside it for buyers who prefer it, and a dedicated account like Easy Pay Direct only if automated processors keep flagging you.

If you’re on Shopify instead, see our best payment processor for Shopify comparison.

Head-to-Head Comparison

When not to use each:

• WooPayments isn’t available in every country, and since it’s built on Stripe, its restricted-business rules generally follow Stripe’s.
• The Stripe plugin requires your own Stripe account and the same restricted-business rules.
• PayPal can place holds on new or unusual activity, which can strain cash flow for a brand-new store.
• Easy Pay Direct takes a few business days to approve, so it isn’t the right fit if you need to sell today.

You might also like: What are the Best Dropshipping Suppliers for Shopify? 

What Each Option Actually Costs

The headline rate is rarely the whole story. International sales add fees, and the fixed per-transaction fee matters more at lower order values. 

Here’s what a $100 sale costs, plus a monthly total at $10,000 in domestic sales, roughly 167 orders at a $60 average:

WooCommerce itself adds no platform fee, so unlike on Shopify, there’s no extra surcharge layered on top of any of these processors. WooPayments publishes its fees country by country, and its international and currency-conversion fees can differ from Stripe’s direct pricing, so check its fee documentation if you sell abroad. And Easy Pay Direct’s rate is only part of its cost, since the setup and monthly fees add to it.

To see how these costs hit your margin on a specific product, use our eCommerce profit calculator. For deeper breakdowns, see our guides to Stripe’s cross-border fees and PayPal’s cross-border fees.

Setup & Compatibility on WooCommerce

Each payment processor connects differently, and the setup effort varies more than the rates do.

1. WooPayments

WooPayments is WooCommerce’s own payment solution, built on Stripe and managed inside your WordPress dashboard, including refunds, disputes, and payouts. It supports WooPay, Apple Pay, Google Pay, Link, and Amazon Pay, plus built-in multi-currency support, and it works with the WooCommerce Subscriptions extension for recurring billing.

2. Stripe

The official WooCommerce Stripe Payment Gateway plugin connects your own Stripe account through OAuth, with webhooks configured automatically. It offers 23 payment methods and 135+ currencies. Our guide to adding Stripe to WooCommerce walks through the setup and the choice between the plugin and WooPayments.

3. PayPal

The WooCommerce PayPal Payments plugin adds PayPal checkout, Pay Later, Venmo, and guest card payments. Our guide to adding PayPal to WooCommerce covers setup, fees, and troubleshooting.

4. Easy Pay Direct

Easy Pay Direct offers an official EPD Commerce Gateway plugin that connects with a single API key and works with WooCommerce Subscriptions. You need an approved merchant account first, which our guide to adding Easy Pay Direct to WooCommerce explains in full.

Considerations to Make When You Choose a Payment Processor

Aside from fees and compatibility with your eCommerce platform, several facets of your operations need to be considered. Here’s what to keep in mind when choosing a payment processor. 

Approval, Underwriting, & High-Risk Stores

WooPayments, Stripe, and PayPal approve accounts largely through automated risk scoring. That’s fast when it works, but it also means flags and freezes can happen with limited human review, and categories like cannabis, CBD, firearms, and adult content are generally restricted. Easy Pay Direct takes the opposite approach, with individual underwriting matched to a bank that already works with your industry, which tends to mean more stability once you’re approved.

Dropshipping and print-on-demand sit in the middle. Plenty of smaller stores process through WooPayments, Stripe, or PayPal without issue, but long overseas shipping windows push up item-not-received disputes, and a rising dispute rate is what usually triggers holds as you grow. 

Our guides to why Stripe holds funds and why PayPal holds funds cover the triggers.

Chargebacks, Disputes, & Account Stability

Dispute fees differ more than most sellers expect. PayPal charges $15 on a standard dispute, refunded if you win, or $20 if it’s filed as a card chargeback. Stripe charges $15 when a dispute is received and not returned, plus another $15 if you respond, which comes back if you win. WooPayments publishes its dispute fees by country, and Easy Pay Direct’s vary by account. Our guides to Stripe’s chargeback fees and PayPal’s chargeback fees break down exactly what’s returned.

On the tooling side, Chargeflow can automate dispute management for WooCommerce stores, and they only charge when they win a dispute.

Payout Timing &Cash Flow

Timing differs more than rates do, and it matters most for new stores.

• WooPayments → a 7-day waiting period after your first successful payment, then payouts follow your schedule, with a pending period of about 2 business days in the US.
• Stripe → typically 7 to 14 days for the first payout, which Stripe says can’t be waived.
• PayPal → funds land in your PayPal balance right away, with 1 to 3 business days to reach your bank, though new or unusual activity can trigger holds.
• Easy Pay Direct → varies by underwriting.

Where your cash flow is concerned, WooPayments gets new stores paid fastest among the automated options. But, whichever you choose, plan for a gap between your first sales and your first payout.

Payment Methods Beyond Cards

All four support the basics, and the wallet and financing options differ. WooPayments and Stripe support digital wallets like Apple Pay and Google Pay, while PayPal adds its own wallet, Pay Later in seven countries, and Venmo in the US.

Buy-now-pay-later options like Affirm, Afterpay, and Klarna are available through WooPayments and Stripe, but they cost more than cards. WooPayments lists Affirm at 6.00% + $0.30 and Klarna at 5.99% + $0.30 for US merchants, and availability depends on your account country. 

If you sell durable goods like furniture, electronics, or appliances to US shoppers, Katapult can be a useful complement to Affirm. It enables you to run lease-to-own for shoppers with low or limited credit, and has an official WooCommerce extension. It’s US-only and unavailable in a few states, so check its documentation before you install it.

Running More Than One Processor

This is a real advantage over some other platforms. Shopify allows only one third-party card provider at a time, but WooCommerce lets you run multiple gateways side-by-side, so customers can choose at checkout. Many stores pair a card processor with PayPal, which also acts as a backup if one processor flags or pauses your account.

How to Switch Processors Without Breaking Things

If you’re moving from one processor to another, saved cards and active subscriptions tied to your old gateway generally don’t transfer automatically, so customers may need to re-enter payment details. 

Before you switch, ask your new processor whether it can import existing customer payment tokens: 

1. Test the new gateway in sandbox mode.
2. Consider running both processors briefly rather than flipping a single switch. 
3. Give active subscribers a heads-up so a failed renewal doesn’t catch them off guard.

These steps can help you create a smooth transition. 

Final Thoughts

There’s no single best payment processor for every WooCommerce store. The right choice depends on your risk category, where your customers are, how fast you need to get paid, and how much cost you’re willing to trade for simplicity. Start with the option that matches your situation, add a second processor for resilience, and run the numbers on your own volume before you commit.

To ideate, plan, and launch an online business from scratch, claim your free Aurajinn launch dashboard today.

Frequently Asked Questions About WooCommerce Payment Processors