diff --git src/wp-includes/class-wp-customize-nav-menus.php src/wp-includes/class-wp-customize-nav-menus.php
index 7d32cbb..4335834 100644
--- src/wp-includes/class-wp-customize-nav-menus.php
+++ src/wp-includes/class-wp-customize-nav-menus.php
@@ -771,6 +771,12 @@ final class WP_Customize_Nav_Menus {
 			( empty( $args['fallback_cb'] ) || is_string( $args['fallback_cb'] ) )
 			&&
 			( empty( $args['walker'] ) || is_string( $args['walker'] ) )
+			&&
+			(
+				! empty( $args['theme_location'] )
+				||
+				( ! empty( $args['menu'] ) && ( is_numeric( $args['menu'] ) || is_object( $args['menu'] ) ) )
+			)
 		);
 		$args['can_partial_refresh'] = $can_partial_refresh;
 
@@ -779,6 +785,11 @@ final class WP_Customize_Nav_Menus {
 			$args['walker'] = '';
 		}
 
+		// Replace object menu arg with a term_id menu arg, as this exports better to JS and is easier to compare hashes.
+		if ( ! empty( $args['menu'] ) && is_object( $args['menu'] ) ) {
+			$args['menu'] = $args['menu']->term_id;
+		}
+
 		ksort( $args );
 		$args['args_hash'] = $this->hash_nav_menu_args( $args );
 
@@ -799,10 +810,11 @@ final class WP_Customize_Nav_Menus {
 	 */
 	public function filter_wp_nav_menu( $nav_menu_content, $args ) {
 		if ( ! empty( $args->can_partial_refresh ) && ! empty( $args->instance_number ) ) {
-			$nav_menu_content = sprintf(
-				'<div id="partial-refresh-menu-container-%1$d" class="partial-refresh-menu-container" data-instance-number="%1$d">%2$s</div>',
-				$args->instance_number,
-				$nav_menu_content
+			$nav_menu_content = preg_replace(
+				'/(?<=class=")/',
+				sprintf( 'partial-refreshable-nav-menu partial-refreshable-nav-menu-%1$d ', $args->instance_number ),
+				$nav_menu_content,
+				1 // Only update the class on the first element found, the menu container.
 			);
 		}
 		return $nav_menu_content;
diff --git src/wp-includes/js/customize-preview-nav-menus.js src/wp-includes/js/customize-preview-nav-menus.js
index 2b6c994..bb8e792 100644
--- src/wp-includes/js/customize-preview-nav-menus.js
+++ src/wp-includes/js/customize-preview-nav-menus.js
@@ -163,19 +163,27 @@ wp.customize.menusPreview = ( function( $, api ) {
 	 * @param {int} instanceNumber
 	 */
 	self.refreshMenuInstance = function( instanceNumber ) {
-		var self = this, data, customized, container, request, wpNavArgs, instance;
+		var self = this, data, menuId, customized, container, request, wpNavArgs, instance, containerInstanceClassName;
 
 		if ( ! self.navMenuInstanceArgs[ instanceNumber ] ) {
 			throw new Error( 'unknown_instance_number' );
 		}
 		instance = self.navMenuInstanceArgs[ instanceNumber ];
 
-		container = $( '#partial-refresh-menu-container-' + String( instanceNumber ) );
+		containerInstanceClassName = 'partial-refreshable-nav-menu-' + String( instanceNumber );
+		container = $( '.' + containerInstanceClassName );
 
-		if ( ! instance.can_partial_refresh || 0 === container.length ) {
+		if ( _.isNumber( instance.menu ) ) {
+			menuId = instance.menu;
+		} else if ( instance.theme_location && api.has( 'nav_menu_locations[' + instance.theme_location + ']' ) ) {
+			menuId = api( 'nav_menu_locations[' + instance.theme_location + ']' ).get();
+		}
+
+		if ( ! menuId || ! instance.can_partial_refresh || 0 === container.length ) {
 			api.preview.send( 'refresh' );
 			return;
 		}
+		menuId = parseInt( menuId, 10 );
 
 		data = {
 			nonce: self.previewCustomizeNonce, // for Customize Preview
@@ -187,8 +195,8 @@ wp.customize.menusPreview = ( function( $, api ) {
 		data[ self.renderQueryVar ] = '1';
 		customized = {};
 		api.each( function( setting, id ) {
-			// @todo We need to limit this to just the menu items that are associated with this menu/location.
-			if ( /^(nav_menu|nav_menu_locations)/.test( id ) ) {
+			// @todo Core should propagate the dirty state into the Preview as well so we can use that here.
+			if ( id === 'nav_menu[' + String( menuId ) + ']' || ( /^nav_menu_item\[/.test( id ) && setting() && menuId === setting().nav_menu_term_id ) ) {
 				customized[ id ] = setting.get();
 			}
 		} );
@@ -207,19 +215,25 @@ wp.customize.menusPreview = ( function( $, api ) {
 			url: self.requestUri
 		} );
 		request.done( function( data ) {
-			var eventParam;
-			container.empty().append( $( data ) );
+			// If the menu is now not visible, refresh since the page layout may have changed.
+			if ( false === data ) {
+				api.preview.send( 'refresh' );
+				return;
+			}
+
+			var eventParam, previousContainer = container;
+			container = $( data );
+			container.addClass( containerInstanceClassName );
+			container.addClass( 'partial-refreshable-nav-menu customize-partial-refreshing' );
+			previousContainer.replaceWith( container );
 			eventParam = {
 				instanceNumber: instanceNumber,
-				wpNavArgs: wpNavArgs
+				wpNavArgs: wpNavArgs,
+				oldContainer: previousContainer,
+				newContainer: container
 			};
-			$( document ).trigger( 'customize-preview-menu-refreshed', [ eventParam ] );
-		} );
-		request.fail( function() {
-			// @todo provide some indication for why
-		} );
-		request.always( function() {
 			container.removeClass( 'customize-partial-refreshing' );
+			$( document ).trigger( 'customize-preview-menu-refreshed', [ eventParam ] );
 		} );
 	};