diff --git a/includes/class-amp-theme-support.php b/includes/class-amp-theme-support.php
index eed6ec0cd31..09c62518338 100644
--- a/includes/class-amp-theme-support.php
+++ b/includes/class-amp-theme-support.php
@@ -504,13 +504,7 @@ public static function get_template_availability( $query = null ) {
 			if ( $is_match ) {
 				$matching_templates[ $id ] = array(
 					'template'  => $id,
-					'supported' => (
-						! empty( $supportable_template['supported'] )
-						||
-						( AMP_Options_Manager::get_option( 'all_templates_supported' ) && empty( $supportable_template['immutable'] ) )
-						||
-						$all_templates_supported_by_theme_support // Make sure theme support flag is given final say.
-					),
+					'supported' => ! empty( $supportable_template['supported'] ),
 					'immutable' => ! empty( $supportable_template['immutable'] ),
 				);
 			}
@@ -692,16 +686,6 @@ public static function get_supportable_templates() {
 			);
 		}
 
-		// Pre-populate template supported state by theme support flag.
-		$theme_support_args = self::get_theme_support_args( array( 'initial' => true ) );
-		if ( isset( $theme_support_args['templates_supported'] ) && is_array( $theme_support_args['templates_supported'] ) ) {
-			foreach ( $templates as $id => &$template ) {
-				if ( isset( $theme_support_args['templates_supported'][ $id ] ) ) {
-					$templates[ $id ]['supported'] = $theme_support_args['templates_supported'][ $id ];
-				}
-			}
-		}
-
 		/**
 		 * Filters list of supportable templates.
 		 *
@@ -721,11 +705,34 @@ public static function get_supportable_templates() {
 		 */
 		$templates = apply_filters( 'amp_supportable_templates', $templates );
 
+		// Obtain the initial template supported state by theme support flag.
+		$theme_support_args        = self::get_theme_support_args( array( 'initial' => true ) );
+		$theme_supported_templates = array();
+		if ( isset( $theme_support_args['templates_supported'] ) ) {
+			$theme_supported_templates = $theme_support_args['templates_supported'];
+		}
+
 		$supported_templates = AMP_Options_Manager::get_option( 'supported_templates' );
 		foreach ( $templates as $id => &$template ) {
+
+			// Capture user-elected support from options. This allows us to preserve the original user selection through programmatic overrides.
+			$template['user_supported'] = in_array( $id, $supported_templates, true );
+
+			// Consider supported templates from theme support args.
+			if ( ! isset( $template['supported'] ) ) {
+				if ( 'all' === $theme_supported_templates ) {
+					$template['supported'] = true;
+				} elseif ( is_array( $theme_supported_templates ) && isset( $theme_supported_templates[ $id ] ) ) {
+					$template['supported'] = $theme_supported_templates[ $id ];
+				}
+			}
+
+			// Make supported state immutable if it was programmatically set.
 			$template['immutable'] = isset( $template['supported'] );
+
+			// Set supported state from user preference.
 			if ( ! $template['immutable'] ) {
-				$template['supported'] = AMP_Options_Manager::get_option( 'all_templates_supported' ) || in_array( $id, $supported_templates, true );
+				$template['supported'] = AMP_Options_Manager::get_option( 'all_templates_supported' ) || $template['user_supported'];
 			}
 		}
 
diff --git a/includes/options/class-amp-options-manager.php b/includes/options/class-amp-options-manager.php
index 6dee88a3046..fd052b5f93d 100644
--- a/includes/options/class-amp-options-manager.php
+++ b/includes/options/class-amp-options-manager.php
@@ -24,7 +24,7 @@ class AMP_Options_Manager {
 	 */
 	protected static $defaults = array(
 		'theme_support'                    => 'disabled',
-		'supported_post_types'             => array( 'post' ),
+		'supported_post_types'             => array( 'post' ), // @todo Try updating from 0.7 to 1.0.
 		'analytics'                        => array(),
 		'force_sanitization'               => false,
 		'accept_tree_shaking'              => false,
@@ -32,7 +32,7 @@ class AMP_Options_Manager {
 		'all_templates_supported'          => true,
 		'unrecognized_templates_supported' => true,
 		'supported_templates'              => array(
-			'is_singular',
+			'is_singular', // @todo Why?
 		),
 	);
 
@@ -132,6 +132,7 @@ public static function validate_options( $new_options ) {
 				$options['unrecognized_templates_supported'] = ! empty( $new_options['unrecognized_templates_supported'] );
 			}
 
+			// @todo Store associative array instead?
 			// Validate post type support.
 			$options['supported_post_types'] = array();
 			if ( isset( $new_options['supported_post_types'] ) ) {
@@ -144,6 +145,7 @@ public static function validate_options( $new_options ) {
 				}
 			}
 
+			// @todo Store associative array instead.
 			// Validate supported templates.
 			$options['supported_templates'] = array();
 			if ( isset( $new_options['supported_templates'] ) ) {
diff --git a/includes/options/class-amp-options-menu.php b/includes/options/class-amp-options-menu.php
index da1ad1a895f..5c5b70557f5 100644
--- a/includes/options/class-amp-options-menu.php
+++ b/includes/options/class-amp-options-menu.php
@@ -419,14 +419,25 @@ private function list_template_conditional_options( $options, $parent = null ) {
 
 				?>
 				<li>
-					<input
-						type="checkbox"
-						id="<?php echo esc_attr( $element_id ); ?>"
-						name="<?php echo esc_attr( $element_name ); ?>"
-						value="<?php echo esc_attr( $id ); ?>"
-						<?php checked( ! empty( $option['supported'] ) ); ?>
-						<?php disabled( ! empty( $option['immutable'] ) ); ?>
-					>
+					<?php if ( empty( $option['immutable'] ) ) : ?>
+						<input
+							type="checkbox"
+							id="<?php echo esc_attr( $element_id ); ?>"
+							name="<?php echo esc_attr( $element_name ); ?>"
+							value="<?php echo esc_attr( $id ); ?>"
+							<?php checked( ! empty( $option['user_supported'] ) ); ?>
+						>
+					<?php else : // Persist user selection even when checkbox disabled, when selection forced by theme/filter. ?>
+						<input
+							type="checkbox"
+							id="<?php echo esc_attr( $element_id ); ?>"
+							<?php checked( ! empty( $option['supported'] ) ); ?>
+							<?php disabled( true ); ?>
+						>
+						<?php if ( ! empty( $option['user_supported'] ) ) : ?>
+							<input type="hidden" name="<?php echo esc_attr( $element_name ); ?>" value="<?php echo esc_attr( $id ); ?>">
+						<?php endif; ?>
+					<?php endif; ?>
 					<label for="<?php echo esc_attr( $element_id ); ?>">
 						<?php echo esc_html( $option['label'] ); ?>
 					</label>