Implementing Stripe Checkout in a Headless WooCommerce Store

Payment integration is where most headless WooCommerce projects stall. You've built a beautiful Next.js frontend, wired up the product catalogue via the REST API, and even managed cart sessions — but the moment a customer clicks "Pay", everything gets complicated. The checkout flow that WooCommerce hands you for free in a traditional theme simply doesn't exist in a headless setup. You have to rebuild it, and Stripe is how most teams do it.

This guide covers the three practical approaches to implementing Stripe checkout in a headless WooCommerce store: Stripe Checkout (hosted redirect), Stripe Elements (embedded card form), and the WooCommerce Stripe gateway via REST API. Each has trade-offs around control, PCI compliance, and development effort. We'll walk through when to use each, how webhook handling ties it all together, and the common mistakes that trip teams up.

Why payment is the hardest part of headless

In a traditional WooCommerce store, the checkout page is a server-rendered form that handles payment tokenisation, order creation, stock reduction, email triggers, and redirect — all in a single page load. When you go headless, you lose all of that. Your frontend is a static or server-rendered application with no direct access to WooCommerce's PHP internals.

This means you must handle three concerns that WooCommerce normally manages for you: securely collecting card details, creating an order in WooCommerce with the correct payment status, and confirming the payment was actually captured (not just initiated). Get any one of these wrong and you'll either leak sensitive data, create orphaned orders, or ship products that were never paid for.

Approach 1: Stripe Checkout (hosted redirect)

Stripe Checkout is a Stripe-hosted payment page. Your frontend redirects the customer to Stripe's domain, they enter their card details on Stripe's servers, and Stripe redirects them back to your site with a session ID. You never touch card data — it never reaches your infrastructure at all.

This is the approach we recommend for most headless WooCommerce stores, particularly those migrating from a traditional setup. The integration is straightforward: your Next.js API route (or server action) creates a Stripe Checkout Session with the line items, then returns the session URL to the frontend. The frontend redirects. Stripe handles the rest.

The flow looks like this: customer clicks "Checkout" → your backend creates a Stripe Checkout Session with line items and prices → frontend redirects to Stripe → customer pays → Stripe redirects to your success URL → your webhook handler creates or updates the WooCommerce order.

Approach 2: Stripe Elements (embedded card form)

Stripe Elements gives you a set of pre-built, customisable UI components that render a secure card input directly on your page. The card details are collected inside a Stripe-hosted iframe, so sensitive data still never touches your servers, but the customer stays on your domain throughout the entire checkout flow.

With Elements, you create a PaymentIntent on your backend, pass the client secret to the frontend, and use Stripe.js to render the Payment Element. When the customer submits, Stripe.js confirms the PaymentIntent directly with Stripe's API. Your backend then listens for a webhook to confirm the payment succeeded and creates the WooCommerce order.

This approach is ideal when you've invested heavily in a custom checkout experience and redirecting customers to Stripe would break the flow. It's also the better option if you need a single-page checkout with shipping address, billing address, and payment all on one screen. The trade-off is more frontend code and a more complex integration.

Approach 3: WooCommerce Stripe gateway via REST API

The third approach keeps WooCommerce as the payment processor. Instead of creating Stripe sessions or PaymentIntents directly, you use WooCommerce's REST API to create an order and process payment through the WooCommerce Stripe Payment Gateway plugin. The plugin handles the Stripe integration on the WordPress side.

In practice, you collect a payment method token on the frontend using Stripe.js, then send that token to WooCommerce's order endpoint along with the order details. WooCommerce's Stripe gateway charges the card using the token and updates the order status. This keeps all payment logic inside WooCommerce, which means existing plugins that hook into WooCommerce's payment flow (subscriptions, invoicing, accounting integrations) continue to work.

Choosing the right approach

For most teams building a headless WooCommerce store on a budget, we recommend starting with Stripe Checkout. You can always migrate to Elements later if you need more UI control. The webhook handling and order synchronisation patterns are the same regardless of which approach you choose, so the migration is manageable.

Webhook handling for order confirmation

Regardless of which Stripe integration you choose, webhooks are essential. Never rely solely on the client-side redirect or confirmation to mark orders as paid. Customers close browser tabs, lose connectivity, or navigate away before your success page loads. The webhook is the only reliable signal that payment was captured.

Set up a webhook endpoint in your Next.js application (e.g. /api/webhooks/stripe) that listens for checkout.session.completed (for Stripe Checkout) or payment_intent.succeeded (for Elements). When the event arrives, verify the webhook signature using your Stripe webhook secret, then create or update the corresponding WooCommerce order via the REST API.

Key events to listen for:

Testing with Stripe test mode

Stripe's test mode is one of the best developer experiences in payments. Use your test API keys (prefixed with sk_test_ and pk_test_) and Stripe's test card numbers to simulate every scenario: successful payments, declined cards, 3D Secure challenges, and network errors.

Set up a separate webhook endpoint for test mode using the Stripe CLI's stripe listen --forward-to command. This forwards test webhook events to your local development server without needing a public URL. For staging environments, create a separate webhook endpoint in the Stripe dashboard pointed at your staging domain.

Apple Pay and Google Pay considerations

Both Apple Pay and Google Pay work with all three Stripe integration approaches, but the setup differs. With Stripe Checkout, they're enabled automatically — Stripe detects the customer's device and shows the appropriate wallet button. With Stripe Elements, you use the Payment Request Button element or the newer Payment Element, which handles wallet detection for you.

For Apple Pay, you must verify your domain with Apple by hosting a verification file at /.well-known/apple-developer-merchantid-domain-association. This is straightforward in Next.js — place the file in your public/.well-known/ directory. Google Pay requires no domain verification for test mode but does require registration for production.

Common errors and debugging

After helping teams implement headless WooCommerce Stripe checkout across dozens of stores, these are the issues we see most frequently:

1. Webhook signature verification failures

The most common cause is using the wrong webhook secret. Stripe generates a different signing secret for each webhook endpoint. If you're using stripe listen locally, it gives you a temporary secret (whsec_...) that differs from the one in your Stripe dashboard. Make sure your environment variables match the correct endpoint.

2. Duplicate orders

This happens when both your success page and your webhook handler create orders. Pick one source of truth — the webhook — and use the success page only to display a confirmation. Use Stripe's idempotency keys and your own order reference mapping to prevent duplicates even if the webhook fires twice.

3. Currency mismatches

Stripe expects amounts in the smallest currency unit (pence for GBP, cents for USD). If your WooCommerce product is £29.99, you must pass 2999 to Stripe, not 29.99. This catches out almost every team at least once. Always multiply by 100 for zero-decimal currencies and handle edge cases for currencies like JPY that have no decimal places.

Security checklist

Before going live with any Stripe integration in a headless WooCommerce store, verify every item on this list. Payment security is not optional — a single breach can end a business. If you're following our WooCommerce launch checklist, add these items to it.

Putting it all together

The best headless WooCommerce Stripe checkout integration is the simplest one that meets your requirements. Start with Stripe Checkout if you want to launch quickly and stay out of PCI scope. Move to Stripe Elements when your checkout UX demands it. Fall back to the WooCommerce gateway only when plugin compatibility requires it.

Regardless of approach, invest time in webhook handling, test coverage, and error handling. Payment is the one part of your store that absolutely cannot fail silently. Use Stripe's test mode exhaustively, simulate every failure path, and monitor your webhook delivery success rate in the Stripe dashboard.

If you're planning a migration to headless WooCommerce, payment integration should be the first thing you prototype — not the last. It's the piece most likely to change your architecture decisions, and the piece where mistakes are most costly. Get it right early and the rest of the build will feel straightforward by comparison.