Your payment gateway choice affects every sale your store makes. Get it wrong and you're either leaving money on the table in fees, limiting your customer base, or dealing with a checkout experience that reduces conversions. Here's a practical comparison of the three most common WooCommerce payment gateways.
Fee Comparison
All three charge roughly 2.9% + 30¢ for domestic card transactions. The differences are in the details:
- Stripe: 2.9% + 30¢ domestic. 3.4% + 30¢ manually entered cards. No monthly fee. Instant payouts available (1.5% fee). Best-in-class dispute management.
- PayPal: 2.89% + 49¢ standard. 3.49% + 49¢ for PayPal Credit/Pay Later. No monthly fee. Free PayPal to PayPal transfers. Higher per-transaction fixed fee cuts into small orders more than Stripe.
- Square: 2.6% + 10¢ for in-person (very competitive). 2.9% + 30¢ online. Free point-of-sale hardware for in-person sales. Best if you have a physical retail component.
Setup Complexity in WooCommerce
Stripe is the easiest WooCommerce integration. The official WooCommerce Stripe plugin is well-maintained, supports Apple Pay and Google Pay out of the box, and handles SCA (Strong Customer Authentication) for European customers automatically. Setup takes 15–30 minutes.
PayPal comes bundled with WooCommerce. It's familiar to customers (many people prefer paying via their PayPal balance) and adds no incremental setup for basic use. The newer PayPal Commerce Platform offers more features but is slightly more complex to configure.
Square requires the Square for WooCommerce plugin (free). It syncs inventory between your online WooCommerce store and your Square POS — the killer feature if you also sell in person. Setup is straightforward but requires a Square account.
International Support
Stripe supports 135+ currencies and is available in 46+ countries. It handles currency conversion and supports local payment methods (SEPA, iDEAL, Sofort) for European customers. Best for international stores.
PayPal supports 25 currencies and works in 200+ countries. The customer-facing PayPal brand is trusted globally, which can improve conversion rates in some markets.
Square is US, Canada, UK, Australia, Japan, and Ireland only. Not suitable for international stores outside these markets.
Which Gateway to Choose
Choose Stripe if: You want the best developer experience, you sell internationally, you want Apple Pay and Google Pay, or you value detailed analytics and reporting.
Choose PayPal if: Your customers frequently pay via PayPal balance (common in certain demographics), you want the trust of the PayPal brand, or you're selling lower-priced items where PayPal's customer recognition increases conversions.
Choose Square if: You also sell in person and need inventory sync between online and physical retail.
Use multiple: Most stores benefit from offering both Stripe (card payments) and PayPal (PayPal account payments). WooCommerce supports multiple active gateways.
Common Integration Problems to Avoid
- Stripe webhooks: Make sure your webhook endpoint is correctly configured in the Stripe dashboard. Webhook failures cause order status issues.
- PayPal IPN: Instant Payment Notification settings can get misconfigured after a site migration. Test a complete transaction after any migration.
- SSL requirement: All three gateways require HTTPS. An expired or misconfigured SSL certificate will silently break payment processing.
- Test mode: Always test with the gateway's sandbox/test mode using test card numbers before going live. Never test with real transactions.
Frequently Asked Questions
Can I use multiple payment gateways at the same time on WooCommerce?
Yes — WooCommerce shows all enabled gateways at checkout and lets the customer choose. Most stores benefit from offering at least Stripe and PayPal.
How do I handle payment gateway issues without losing sales?
Having a backup gateway enabled means a customer can switch payment methods if one fails. Also set up email alerts for payment failures so you can investigate quickly.
Do payment gateways charge for refunds?
Stripe returns the processing fee on refunds. PayPal keeps the fee on refunds. Square returns the processing fee for full refunds but not partial refunds. This matters if your return rate is high.
What's the easiest way to get set up correctly the first time?
Start with Stripe — the WooCommerce integration is the most reliable and best maintained. Our WooCommerce integration service includes full payment gateway configuration and testing as standard.