diff --git a/changelog/migration-stripe-link-disablement-with-woopay-enabled b/changelog/migration-stripe-link-disablement-with-woopay-enabled
new file mode 100644
index 00000000000..169afd3ee5e
--- /dev/null
+++ b/changelog/migration-stripe-link-disablement-with-woopay-enabled
@@ -0,0 +1,4 @@
+Significance: minor
+Type: add
+
+Add migration script to cover situations with Link and WooPay both enabled after plugin update.
diff --git a/includes/class-wc-payments.php b/includes/class-wc-payments.php
index 2f73ad342e6..a0f14bd38aa 100644
--- a/includes/class-wc-payments.php
+++ b/includes/class-wc-payments.php
@@ -587,11 +587,13 @@ public static function init() {
 		require_once __DIR__ . '/migrations/class-allowed-payment-request-button-sizes-update.php';
 		require_once __DIR__ . '/migrations/class-update-service-data-from-server.php';
 		require_once __DIR__ . '/migrations/class-additional-payment-methods-admin-notes-removal.php';
+		require_once __DIR__ . '/migrations/class-link-woopay-mutual-exclusion-handler.php';
 		require_once __DIR__ . '/migrations/class-delete-active-woopay-webhook.php';
 		add_action( 'woocommerce_woocommerce_payments_updated', [ new Allowed_Payment_Request_Button_Types_Update( self::get_gateway() ), 'maybe_migrate' ] );
 		add_action( 'woocommerce_woocommerce_payments_updated', [ new \WCPay\Migrations\Allowed_Payment_Request_Button_Sizes_Update( self::get_gateway() ), 'maybe_migrate' ] );
 		add_action( 'woocommerce_woocommerce_payments_updated', [ new \WCPay\Migrations\Update_Service_Data_From_Server( self::get_account_service() ), 'maybe_migrate' ] );
 		add_action( 'woocommerce_woocommerce_payments_updated', [ new \WCPay\Migrations\Additional_Payment_Methods_Admin_Notes_Removal(), 'maybe_migrate' ] );
+		add_action( 'woocommerce_woocommerce_payments_updated', [ new \WCPay\Migrations\Link_WooPay_Mutual_Exclusion_Handler( self::get_gateway() ), 'maybe_migrate' ] );
 		add_action( 'woocommerce_woocommerce_payments_updated', [ '\WCPay\Migrations\Delete_Active_WooPay_Webhook', 'maybe_delete' ] );
 
 		include_once WCPAY_ABSPATH . '/includes/class-wc-payments-explicit-price-formatter.php';
@@ -737,14 +739,6 @@ public static function get_plugin_headers() {
 	public static function register_gateway( $gateways ) {
 		$payment_methods = array_keys( self::get_payment_method_map() );
 
-		$key = array_search( 'link', $payment_methods, true );
-
-		if ( false !== $key && WC_Payments_Features::is_woopay_enabled() ) {
-			unset( $payment_methods[ $key ] );
-
-			self::get_gateway()->update_option( 'upe_enabled_payment_method_ids', $payment_methods );
-		}
-
 		$gateways[]       = self::$card_gateway;
 		$all_gateways     = [];
 		$reusable_methods = [];
diff --git a/includes/migrations/class-link-woopay-mutual-exclusion-handler.php b/includes/migrations/class-link-woopay-mutual-exclusion-handler.php
new file mode 100644
index 00000000000..53284365adb
--- /dev/null
+++ b/includes/migrations/class-link-woopay-mutual-exclusion-handler.php
@@ -0,0 +1,71 @@
+<?php
+/**
+ * Class Link_WooPay_Mutual_Exclusion_Handler
+ *
+ * @package WooCommerce\Payments
+ */
+
+namespace WCPay\Migrations;
+
+use WC_Payment_Gateway_WCPay;
+use WC_Payments_Features;
+
+defined( 'ABSPATH' ) || exit;
+
+/**
+ * Class Link_WooPay_Mutual_Exclusion_Handler
+ *
+ * In version 7.3.0, the logic responsible for disabling Stripe Link if WooPay is by default enabled, is moved from the gateways registration step to the migration.
+ *
+ * @since 7.3.0
+ */
+class Link_WooPay_Mutual_Exclusion_Handler {
+
+	/**
+	 * Version in which this migration was introduced.
+	 *
+	 * @var string
+	 */
+	const VERSION_SINCE = '7.3.0';
+
+	/**
+	 * WCPay gateway.
+	 *
+	 * @var WC_Payment_Gateway_WCPay
+	 */
+	private $gateway;
+
+	/**
+	 * Link_WooPay_Mutual_Exclusion_Handler constructor.
+	 *
+	 * @param WC_Payment_Gateway_WCPay $gateway WCPay gateway.
+	 */
+	public function __construct( WC_Payment_Gateway_WCPay $gateway ) {
+		$this->gateway = $gateway;
+	}
+
+	/**
+	 * Only execute the migration if not applied yet.
+	 */
+	public function maybe_migrate() {
+		$previous_version = get_option( 'woocommerce_woocommerce_payments_version' );
+		if ( version_compare( self::VERSION_SINCE, $previous_version, '>' ) ) {
+			$this->migrate();
+		}
+	}
+
+	/**
+	 * Does the actual migration as described in the class docblock.
+	 */
+	private function migrate() {
+		// check if both Stripe Link and WooPay are enabled and if so - disable Stripe Link.
+		$enabled_payment_methods   = $this->gateway->get_payment_method_ids_enabled_at_checkout();
+		$enabled_stripe_link_index = array_search( 'link', $enabled_payment_methods, true );
+
+		if ( false !== $enabled_stripe_link_index && WC_Payments_Features::is_woopay_enabled() ) {
+			unset( $enabled_payment_methods[ $enabled_stripe_link_index ] );
+
+			$this->gateway->update_option( 'upe_enabled_payment_method_ids', $enabled_payment_methods );
+		}
+	}
+}