WooCommerce to Shopify: payment gateway migration guide (2026)

Payment gateway migration is one of the most anxiety-inducing parts of moving from WooCommerce to Shopify. There's concern about lost transactions, saved customer payment methods, and whether your specific gateway even works on Shopify. This guide covers everything you need to know.

The short answer: most payment gateways work on both platforms

The major gateways — Stripe, PayPal, Braintree, Authorize.Net, Square — all have official Shopify integrations. If you were using one of these on WooCommerce, the transition is straightforward: install the Shopify app, reconnect your account, and test checkout.

The more complex situation: saved customer payment methods, recurring billing tokens, and country-specific gateways not available on Shopify.

Shopify Payments: the path-of-least-resistance option

Shopify Payments is Shopify's native payment processor (powered by Stripe). For merchants in supported countries, it's often the best Shopify option because:

• No transaction fees on top of Shopify subscription (other gateways incur 0.5–2% Shopify fee)
• Checkout is deeply integrated — no redirect, faster load times
• Chargeback management is built into Shopify admin
• Supports Shop Pay (accelerated checkout), Shop Pay Installments (buy now, pay later)
• Multi-currency selling with automatic conversion

Shopify Payments is available in: United States, Canada, United Kingdom, Australia, New Zealand, Ireland, Germany, Spain, France, Italy, Netherlands, Singapore, Japan, Hong Kong, and others.

If you were using Stripe on WooCommerce

You have two options on Shopify:

1. Shopify Payments (recommended if available in your country): Same underlying Stripe infrastructure, fully integrated, eliminates Shopify transaction fees.
2. Stripe directly: Install the Stripe Shopify app. You'll pay the 0.5–2% Shopify transaction fee on top of Stripe's rates.

Most merchants on Stripe should switch to Shopify Payments — the rate difference (avoiding the Shopify transaction fee) pays for itself quickly at any significant volume.

If you were using PayPal on WooCommerce

PayPal is available as a native integration in Shopify. Install "PayPal Express Checkout" from the Shopify payments section. Your PayPal account connects directly — no re-registration needed.

PayPal is typically offered as a secondary payment option alongside Shopify Payments or your primary card processor, not as the sole gateway.

Transaction fees: WooCommerce vs Shopify

Scenario	WooCommerce	Shopify (Shopify Payments)	Shopify (3rd party gateway)
Basic plan (~$30/mo)	0% platform fee	2% Shopify + gateway %	2% Shopify + gateway %
Shopify plan (~$80/mo)	0% platform fee	1% Shopify + gateway %	1% Shopify + gateway %
Advanced plan (~$300/mo)	0% platform fee	0.5% Shopify + gateway %	0.5% Shopify + gateway %
Shopify Payments	N/A	0% Shopify fee (uses SP)	N/A

If you're using Shopify Payments, there's no Shopify transaction fee — you only pay Shopify Payments processing rates (2.4–2.9% + 30¢ for cards in the US, varies by country and plan). If you're using a third-party gateway, Shopify charges 0.5–2% on top of whatever the gateway charges.

For most merchants doing meaningful volume, Shopify Payments is the clear choice if available in your country. The savings on transaction fees typically cover the difference in monthly plan cost within a few months.

Saved customer payment methods

This is the key concern for stores with repeat customers or subscriptions: can saved payment methods (credit cards on file) be transferred from WooCommerce to Shopify?

Short answer: No, not automatically.

WooCommerce stores payment tokens (references to stored cards) in its own database, tied to the specific payment gateway account. When you switch gateways or platforms:

• If switching from Stripe on WooCommerce to Shopify Payments (same Stripe account): You may be able to transfer customer Stripe tokens, but it requires custom development and API work on both ends. Not supported by migration tools.
• If switching payment processors entirely: No path to transfer stored cards. Customers must re-enter payment information.

For stores without subscriptions (one-time purchases), this is a minor inconvenience — customers re-enter their card on first Shopify purchase. For subscription businesses, this is a major issue (see the subscriptions migration guide for handling this).

What happens during the transition period

While your domain is pointing to WooCommerce but you're testing Shopify on a staging URL:

• Your WooCommerce gateway processes all orders
• Test Shopify checkout with Shopify's test mode (no real charges)
• Before DNS switch: enable your payment gateway on Shopify and run one real test transaction

After DNS switch:

• All new orders process through Shopify's gateway
• Keep WooCommerce gateway active for any delayed order processing (refunds, chargebacks) for 60–90 days
• Don't cancel your old gateway account immediately — you need it for refunds on orders placed before the switch

Country-specific gateways not available on Shopify

Shopify's gateway support is excellent but not universal. If you were using a regional gateway that Shopify doesn't support, you'll need an alternative. Common situations:

• iDEAL (Netherlands): Available on Shopify via Mollie or Adyen integrations
• SOFORT (Germany/Austria): Available via Stripe or Klarna on Shopify
• Klarna (multiple countries): Klarna has a native Shopify app
• Afterpay/Clearpay: Native Shopify integration available
• Boleto (Brazil): Available via PagSeguro or Pagar.me Shopify apps
• OXXO (Mexico): Available via Conekta or Stripe Shopify integrations
• PayU (Eastern Europe/India/LatAm): Official PayU Shopify app available

If your gateway is not on this list, check the Shopify App Store for your specific payment method. If there's no Shopify integration, you'll need to either switch to a supported gateway or use Shopify Plus (which allows custom payment gateways via Shopify Scripts).

Checklist: payment setup before launch

• Decide on primary gateway (Shopify Payments if available, else Stripe direct, etc.)
• Install and connect gateway to your Shopify store
• Enable any secondary gateways (PayPal, buy-now-pay-later, etc.)
• Configure currency settings (if selling internationally)
• Run test transaction in Shopify's test mode
• Run real test transaction (small amount — refund after)
• Verify order confirmation email triggers on test purchase
• Verify payout settings (bank account connected, payout schedule)
• Confirm 3D Secure / SCA settings comply with your local requirements (EU stores)
• Keep old WooCommerce gateway active for 60–90 days after cutover for refunds

Tax collection after migration

Payment gateway migration is tightly linked to tax setup. When you switch platforms, your tax configuration starts fresh. WooCommerce tax rules don't carry over to Shopify.

In Shopify, you have options:

• Shopify Tax: Free for US sellers, uses Shopify's tax calculation engine (good for US multi-state compliance)
• TaxJar: $19/mo, deep US sales tax automation with economic nexus tracking
• Avalara AvaTax: Enterprise pricing, handles US + international VAT/GST
• Manual tax rates: For stores with simple, known tax obligations

Set up tax collection before going live. Collecting the wrong tax amount (or failing to collect at all) creates compliance issues and potential liability.