Shopify payment gateways after migrating from WooCommerce (2026)
How to choose and set up payment gateways on Shopify after WooCommerce — Shopify Payments vs Stripe vs PayPal, transaction fees, BACS and bank transfer, UK payment options, and replacing WooCommerce payment plugins.
Payment gateway setup is one of the first decisions when migrating from WooCommerce to Shopify. WooCommerce is gateway-agnostic — you install whatever plugin you need. Shopify has its own payment solution (Shopify Payments) and charges transaction fees when you use an external gateway. Understanding this fee structure before choosing your payment setup can save significant money.
Shopify's payment fee structure
Shopify charges two types of fees on transactions:
- Payment processing fee: A percentage charged by whichever payment gateway processes the card. This applies regardless of which gateway you use.
- Shopify transaction fee: An additional fee Shopify charges when you use an external payment gateway (not Shopify Payments). This is 0.5%–2% depending on your Shopify plan — and it applies on top of the gateway's own processing fee.
If you use Shopify Payments, the Shopify transaction fee is waived. This is the primary reason most UK merchants use Shopify Payments.
Shopify Payments (UK)
Shopify Payments is Shopify's own payment solution, powered by Stripe. It's available to eligible UK merchants:
- No Shopify transaction fee (0% on top of processing)
- Processing rates (as of 2026): Basic plan 2.0%, Shopify plan 1.7%, Advanced plan 1.5% (online card transactions)
- Payouts: next business day to UK bank accounts
- Supports: Visa, Mastercard, Amex, Apple Pay, Google Pay, Shop Pay
- Chargebacks managed within Shopify admin
Shopify Payments is not available for certain product categories (adult content, specific financial services, some supplements). Check Shopify's prohibited business types list before assuming eligibility.
External payment gateways and transaction fees
If you use an external gateway (Stripe, PayPal, SagePay, Worldpay), Shopify adds a transaction fee:
| Shopify plan | Transaction fee (external gateway) |
|---|---|
| Basic | 2.0% |
| Shopify | 1.0% |
| Advanced | 0.5% |
| Plus | 0.15% |
At Basic plan, using Stripe (1.5% + 20p per transaction) means total fees of 3.5% + 20p — significantly higher than Shopify Payments at 2.0%. Unless you have a specific reason to use an external gateway, Shopify Payments is almost always better value for UK merchants.
WooCommerce payment plugin equivalents
| WooCommerce plugin | Shopify equivalent | Notes |
|---|---|---|
| WooCommerce Payments | Shopify Payments | Both powered by Stripe |
| WooCommerce Stripe Gateway | Stripe (external gateway) | Incurs Shopify transaction fee; use Shopify Payments instead |
| WooCommerce PayPal | PayPal (Shopify app) | Available; incurs transaction fee unless on Plus |
| Klarna for WooCommerce | Klarna (via Shopify Payments) | Available in Shopify Payments on eligible plans |
| WooCommerce BACS (bank transfer) | Bank deposit (manual payment) | Configure in Shopify Settings → Payments → Manual payment methods |
| WooCommerce Cash on Delivery | Cash on Delivery (manual) | Same location in Shopify |
| SagePay / Opayo | Opayo (external gateway) | Available; incurs transaction fee |
Buy now, pay later (BNPL) on Shopify
Buy now, pay later options are available through Shopify Payments and external providers:
- Klarna: Available via Shopify Payments for eligible merchants. Pay in 3, Pay in 30 days.
- Clearpay (Afterpay): Available as an external payment provider. Note: Shopify transaction fee applies unless on Plus plan.
- PayPal Pay Later: Included with PayPal integration.
- BNPL typically increases average order value by 20–30% — worth configuring for relevant product types (furniture, electronics, fashion).
BACS and bank transfer on Shopify
WooCommerce has BACS (Bankers' Automated Clearing Services) as a built-in payment method. Shopify's equivalent is Bank Deposit under Manual Payment Methods:
- Settings → Payments → Manual payment methods → Add manual payment method → Bank deposit
- Add your bank account details (sort code, account number, reference instructions) in the instructions field
- Orders placed via bank deposit have status "payment pending" until you manually mark as paid
- Useful for B2B/trade customers who prefer BACS; less suitable for consumer retail
Multi-currency
Shopify Payments supports multi-currency on Shopify and above plans:
- Enable Markets in Shopify admin to sell in multiple currencies
- Shopify converts prices automatically at current exchange rates with an optional rounding rule
- WooCommerce multi-currency plugins (WPML, Aelia Currency Switcher) have no direct equivalent — Shopify's native Markets replaces them
- Payouts are always in your home currency (GBP for UK merchants) — currency conversion happens on Shopify's side
Post-migration payment checklist
- Shopify Payments eligibility confirmed (product types, business type)
- Shopify Payments enabled and bank account connected for payouts
- Test card transaction placed and refunded to confirm setup
- PayPal added if significant proportion of customers use it (typically 15–25% of UK checkout preference)
- BACS/bank deposit configured if serving trade customers
- BNPL option (Klarna/Clearpay) enabled if average order value justifies it
- Transaction fee impact calculated — confirm external gateways still cost-effective vs switching to Shopify Payments
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