diff --git a/projects/packages/waf/changelog/fix-waf-ensure-mode-option-set b/projects/packages/waf/changelog/fix-waf-ensure-mode-option-set
new file mode 100644
index 0000000000000..0af8132fdb0d1
--- /dev/null
+++ b/projects/packages/waf/changelog/fix-waf-ensure-mode-option-set
@@ -0,0 +1,4 @@
+Significance: patch
+Type: fixed
+
+WAF: Ensure mode option is set during activation
diff --git a/projects/packages/waf/src/class-waf-initializer.php b/projects/packages/waf/src/class-waf-initializer.php
index c2720f83ca7cf..1433dcfe14090 100644
--- a/projects/packages/waf/src/class-waf-initializer.php
+++ b/projects/packages/waf/src/class-waf-initializer.php
@@ -42,6 +42,9 @@ public static function init() {
 		// Update the WAF after installing or upgrading a relevant Jetpack plugin
 		add_action( 'upgrader_process_complete', __CLASS__ . '::update_waf_after_plugin_upgrade', 10, 2 );
 
+		// Update the WAF after updating the rules settings
+		Waf_Rules_Manager::add_hooks();
+
 		// Check for compatibility updates
 		add_action( 'admin_init', __CLASS__ . '::check_for_updates' );
 
@@ -49,6 +52,9 @@ public static function init() {
 		add_action( 'jetpack_activate_module_waf', __CLASS__ . '::on_waf_activation' );
 		add_action( 'jetpack_deactivate_module_waf', __CLASS__ . '::on_waf_deactivation' );
 
+		// Update the WAF rule files on a schedule
+		Waf_Rules_Manager::schedule_rules_cron();
+
 		// Brute force protection activation/deactivation hooks
 		add_action( 'jetpack_activate_module_protect', __CLASS__ . '::on_brute_force_protection_activation' );
 		add_action( 'jetpack_deactivate_module_protect', __CLASS__ . '::on_brute_force_protection_deactivation' );
@@ -68,9 +74,6 @@ public static function init() {
 	 * @return bool|WP_Error True if the WAF activation is successful, WP_Error otherwise.
 	 */
 	public static function on_waf_activation() {
-		update_option( Waf_Runner::MODE_OPTION_NAME, 'normal' );
-		add_option( Waf_Rules_Manager::AUTOMATIC_RULES_ENABLED_OPTION_NAME, false );
-
 		try {
 			Waf_Runner::activate();
 			( new Waf_Standalone_Bootstrap() )->generate();
diff --git a/projects/packages/waf/src/class-waf-runner.php b/projects/packages/waf/src/class-waf-runner.php
index c1a8eb1965057..7747335ac5c82 100644
--- a/projects/packages/waf/src/class-waf-runner.php
+++ b/projects/packages/waf/src/class-waf-runner.php
@@ -37,12 +37,7 @@ public static function initialize() {
 		if ( ! self::is_allowed_mode( JETPACK_WAF_MODE ) ) {
 			return;
 		}
-		// Don't run if in standalone mode
-		if ( function_exists( 'add_action' ) ) {
-			self::add_hooks();
-			Waf_Rules_Manager::add_hooks();
-			Waf_Rules_Manager::schedule_rules_cron();
-		}
+
 		if ( ! self::did_run() ) {
 			self::run();
 		}
@@ -52,11 +47,10 @@ public static function initialize() {
 	 * Set action hooks
 	 *
 	 * @return void
+	 *
+	 * @deprecated $$next-version$$ Hooks have been moved to Waf_Initializer class.
 	 */
-	public static function add_hooks() {
-		// Register REST routes.
-		add_action( 'rest_api_init', array( new REST_Controller(), 'register_rest_routes' ) );
-	}
+	public static function add_hooks() {}
 
 	/**
 	 * Did the WAF run yet or not?
@@ -306,7 +300,7 @@ public static function initialize_filesystem() {
 	}
 
 	/**
-	 * Activates the WAF by generating the rules script and setting the version
+	 * Activates the WAF by generating the rules script and setting the related options.
 	 *
 	 * @throws Waf_Exception If the firewall mode is invalid.
 	 * @throws Waf_Exception If the activation fails.
@@ -314,11 +308,16 @@ public static function initialize_filesystem() {
 	 * @return void
 	 */
 	public static function activate() {
-		$version = get_option( Waf_Rules_Manager::VERSION_OPTION_NAME );
-		if ( ! $version ) {
-			add_option( Waf_Rules_Manager::VERSION_OPTION_NAME, Waf_Rules_Manager::RULES_VERSION );
+		// Ensure version and mode options exist and have non-empty values.
+		if ( ! get_option( Waf_Rules_Manager::VERSION_OPTION_NAME ) ) {
+			update_option( Waf_Rules_Manager::VERSION_OPTION_NAME, Waf_Rules_Manager::RULES_VERSION );
+		}
+		if ( ! get_option( self::MODE_OPTION_NAME ) ) {
+			update_option( self::MODE_OPTION_NAME, 'normal' );
 		}
 
+		// Ensure options exist.
+		add_option( Waf_Rules_Manager::AUTOMATIC_RULES_ENABLED_OPTION_NAME, false );
 		add_option( self::SHARE_DATA_OPTION_NAME, true );
 
 		self::initialize_filesystem();