How to Safely Reconcile Stripe and WooCommerce Payment Status Mismatches

When Stripe marks a payment as successful but WooCommerce still shows it as pending or failed, the immediate instinct to manually change the order status can cause fulfillment errors. Developers are advised to first document key data points — including the PaymentIntent ID, amounts, currencies, and webhook timestamps — before making any changes. Because payment updates between WooCommerce and Stripe are not always synchronous, a short grace period of around five minutes is recommended before treating a status gap as an incident. Webhook delivery logs, server responses, and PHP error logs should all be reviewed to determine whether the event was received and processed correctly. Amount comparisons must use normalized values in the currency's smallest unit, and any discrepancy should trigger a thorough investigation rather than an assumption of an overcharge.