diff --git a/src/wp-admin/js/customize-widgets.js b/src/wp-admin/js/customize-widgets.js
index 48ba335138..f2782b98e4 100644
--- a/src/wp-admin/js/customize-widgets.js
+++ b/src/wp-admin/js/customize-widgets.js
@@ -942,6 +942,7 @@
 			params.action = 'update-widget';
 			params.wp_customize = 'on';
 			params.nonce = api.Widgets.data.nonce;
+			params.theme = api.settings.theme.stylesheet;
 
 			data = $.param( params );
 			$inputs = this._getInputs( $widgetContent );
@@ -1614,7 +1615,7 @@
 				widgetNumber = widget.get( 'multi_number' );
 			}
 
-			controlHtml = $( '#widget-tpl-' + widget.get( 'id' ) ).html();
+			controlHtml = $.trim( $( '#widget-tpl-' + widget.get( 'id' ) ).html() );
 			if ( widget.get( 'is_multi' ) ) {
 				controlHtml = controlHtml.replace( /<[^<>]+>/g, function( m ) {
 					return m.replace( /__i__|%i%/g, widgetNumber );
diff --git a/src/wp-includes/class-wp-customize-manager.php b/src/wp-includes/class-wp-customize-manager.php
index 18a1d761c8..8ed4e699a5 100644
--- a/src/wp-includes/class-wp-customize-manager.php
+++ b/src/wp-includes/class-wp-customize-manager.php
@@ -575,6 +575,7 @@ final class WP_Customize_Manager {
 			// to operate properly.
 			$this->stop_previewing_theme();
 			switch_theme( $this->get_stylesheet() );
+			update_option( 'theme_switched_via_customizer', true );
 			$this->start_previewing_theme();
 		}
 
diff --git a/src/wp-includes/class-wp-customize-widgets.php b/src/wp-includes/class-wp-customize-widgets.php
index 5416590b9a..049ceddbfb 100644
--- a/src/wp-includes/class-wp-customize-widgets.php
+++ b/src/wp-includes/class-wp-customize-widgets.php
@@ -60,6 +60,13 @@ final class WP_Customize_Widgets {
 	 */
 	protected $rendered_widgets = array();
 
+	/**
+	 * @since 3.9.0
+	 * @access protected
+	 * @var array
+	 */
+	protected $old_sidebars_widgets = array();
+
 	/**
 	 * Initial loader.
 	 *
@@ -72,6 +79,7 @@ final class WP_Customize_Widgets {
 		$this->manager = $manager;
 
 		add_action( 'after_setup_theme',                       array( $this, 'setup_widget_addition_previews' ) );
+		add_action( 'wp_loaded',                               array( $this, 'override_sidebars_widgets_for_theme_switch' ) );
 		add_action( 'customize_controls_init',                 array( $this, 'customize_controls_init' ) );
 		add_action( 'customize_register',                      array( $this, 'schedule_customize_register' ), 1 );
 		add_action( 'customize_controls_enqueue_scripts',      array( $this, 'enqueue_scripts' ) );
@@ -115,7 +123,6 @@ final class WP_Customize_Widgets {
 	 * @since 3.9.0
 	 *
 	 * @access public
-	 * @global WP_Customize_Manager $wp_customize Customizer instance.
 	 */
 	public function setup_widget_addition_previews() {
 		$is_customize_preview = false;
@@ -125,12 +132,12 @@ final class WP_Customize_Widgets {
 		}
 
 		$is_ajax_widget_update = false;
-		if ( defined( 'DOING_AJAX' ) && DOING_AJAX && 'update-widget' === $this->get_post_value( 'action' ) ) {
+		if ( $this->manager->doing_ajax() && 'update-widget' === $this->get_post_value( 'action' ) ) {
 			$is_ajax_widget_update = check_ajax_referer( 'update-widget', 'nonce', false );
 		}
 
 		$is_ajax_customize_save = false;
-		if ( defined( 'DOING_AJAX' ) && DOING_AJAX && 'customize_save' === $this->get_post_value( 'action' ) ) {
+		if ( $this->manager->doing_ajax() && 'customize_save' === $this->get_post_value( 'action' ) ) {
 			$is_ajax_customize_save = check_ajax_referer( 'save-customize_' . $this->manager->get_stylesheet(), 'nonce', false );
 		}
 
@@ -278,6 +285,72 @@ final class WP_Customize_Widgets {
 		$this->_prepreview_added_filters = array();
 	}
 
+	/**
+	 * Override sidebars_widgets for theme switch.
+	 *
+	 * When switching a theme via the customizer, supply any previously-configured
+	 * sidebars_widgets from the target theme as the initial sidebars_widgets
+	 * setting. Also store the old theme's existing settings so that they can
+	 * be passed along for storing in the sidebars_widgets theme_mod when the
+	 * theme gets switched.
+	 *
+	 * @since 3.9.0
+	 * @access public
+	 */
+	public function override_sidebars_widgets_for_theme_switch() {
+		global $sidebars_widgets;
+
+		if ( $this->manager->doing_ajax() || $this->manager->is_theme_active() ) {
+			return;
+		}
+
+		$this->old_sidebars_widgets = wp_get_sidebars_widgets();
+		add_filter( 'customize_value_old_sidebars_widgets_data', array( $this, 'filter_customize_value_old_sidebars_widgets_data' ) );
+
+		// retrieve_widgets() looks at the global $sidebars_widgets
+		$sidebars_widgets = $this->old_sidebars_widgets;
+		$sidebars_widgets = retrieve_widgets( 'customize' );
+		add_filter( 'option_sidebars_widgets', array( $this, 'filter_option_sidebars_widgets_for_theme_switch' ), 1 );
+	}
+
+	/**
+	 * Filter old_sidebars_widgets_data customizer setting.
+	 *
+	 * When switching themes, filter the Customizer setting
+	 * old_sidebars_widgets_data to supply initial $sidebars_widgets before they
+	 * were overridden by retrieve_widgets(). The value for
+	 * old_sidebars_widgets_data gets set in the old theme's sidebars_widgets
+	 * theme_mod.
+	 *
+	 * @see WP_Customize_Widgets::handle_theme_switch()
+	 * @since 3.9.0
+	 * @access public
+	 *
+	 * @param array $sidebars_widgets
+	 */
+	public function filter_customize_value_old_sidebars_widgets_data( $old_sidebars_widgets ) {
+		return $this->old_sidebars_widgets;
+	}
+
+	/**
+	 * Filter sidebars_widgets option for theme switch.
+	 *
+	 * When switching themes, the retrieve_widgets() function is run when the
+	 * Customizer initializes, and then the new sidebars_widgets here get
+	 * supplied as the default value for the sidebars_widgets option.
+	 *
+	 * @see WP_Customize_Widgets::handle_theme_switch()
+	 * @since 3.9.0
+	 * @access public
+	 *
+	 * @param array $sidebars_widgets
+	 */
+	public function filter_option_sidebars_widgets_for_theme_switch( $sidebars_widgets ) {
+		$sidebars_widgets = $GLOBALS['sidebars_widgets'];
+		$sidebars_widgets['array_version'] = 3;
+		return $sidebars_widgets;
+	}
+
 	/**
 	 * Make sure all widgets get loaded into the Customizer.
 	 *
@@ -349,6 +422,18 @@ final class WP_Customize_Widgets {
 			$new_setting_ids[] = $setting_id;
 		}
 
+		/*
+		 * Add a setting which will be supplied for the theme's sidebars_widgets
+		 * theme_mod when the the theme is switched.
+		 */
+		if ( ! $this->manager->is_theme_active() ) {
+			$setting_id = 'old_sidebars_widgets_data';
+			$setting_args = $this->get_setting_args( $setting_id, array(
+				'type' => 'global_variable',
+			) );
+			$this->manager->add_setting( $setting_id, $setting_args );
+		}
+
 		foreach ( $sidebars_widgets as $sidebar_id => $sidebar_widget_ids ) {
 			if ( empty( $sidebar_widget_ids ) ) {
 				$sidebar_widget_ids = array();
diff --git a/src/wp-includes/theme.php b/src/wp-includes/theme.php
index f66fd95215..00b3c39d1f 100644
--- a/src/wp-includes/theme.php
+++ b/src/wp-includes/theme.php
@@ -752,10 +752,18 @@ function preview_theme_ob_filter_callback( $matches ) {
  * @param string $stylesheet Stylesheet name
  */
 function switch_theme( $stylesheet ) {
-	global $wp_theme_directories, $sidebars_widgets;
+	global $wp_theme_directories, $wp_customize, $sidebars_widgets;
 
-	if ( is_array( $sidebars_widgets ) )
-		set_theme_mod( 'sidebars_widgets', array( 'time' => time(), 'data' => $sidebars_widgets ) );
+	$_sidebars_widgets = null;
+	if ( 'wp_ajax_customize_save' === current_action() ) {
+		$_sidebars_widgets = $wp_customize->post_value( $wp_customize->get_setting( 'old_sidebars_widgets_data' ) );
+	} elseif ( is_array( $sidebars_widgets ) ) {
+		$_sidebars_widgets = $sidebars_widgets;
+	}
+
+	if ( is_array( $_sidebars_widgets ) ) {
+		set_theme_mod( 'sidebars_widgets', array( 'time' => time(), 'data' => $_sidebars_widgets ) );
+	}
 
 	$old_theme  = wp_get_theme();
 	$new_theme = wp_get_theme( $stylesheet );
@@ -782,9 +790,19 @@ function switch_theme( $stylesheet ) {
 
 	update_option( 'current_theme', $new_name );
 
+	// Migrate from the old mods_{name} option to theme_mods_{slug}.
 	if ( is_admin() && false === get_option( 'theme_mods_' . $stylesheet ) ) {
 		$default_theme_mods = (array) get_option( 'mods_' . $new_name );
 		add_option( "theme_mods_$stylesheet", $default_theme_mods );
+	} else {
+		/*
+		 * Since retrieve_widgets() is called when initializing the customizer theme,
+		 * we need to to remove the theme mods to avoid overwriting changes made via
+		 * the widget customizer when accessing wp-admin/widgets.php.
+		 */
+		if ( 'wp_ajax_customize_save' === current_action() ) {
+			remove_theme_mod( 'sidebars_widgets' );
+		}
 	}
 
 	update_option( 'theme_switched', $old_theme->get_stylesheet() );
@@ -1791,6 +1809,12 @@ function check_theme_switched() {
 	if ( $stylesheet = get_option( 'theme_switched' ) ) {
 		$old_theme = wp_get_theme( $stylesheet );
 
+		// Prevent retrieve_widgets() from running since Customizer already called it up front
+		if ( get_option( 'theme_switched_via_customizer' ) ) {
+			remove_action( 'after_switch_theme', '_wp_sidebars_changed' );
+			update_option( 'theme_switched_via_customizer', false );
+		}
+
 		if ( $old_theme->exists() ) {
 			/**
 			 * Fires on the first WP load after a theme switch if the old theme still exists.
@@ -1918,4 +1942,4 @@ function wp_customize_support_script() {
 		}());
 	</script>
 	<?php
-}
\ No newline at end of file
+}
diff --git a/src/wp-includes/widgets.php b/src/wp-includes/widgets.php
index b911fdebf4..4905bbdb07 100644
--- a/src/wp-includes/widgets.php
+++ b/src/wp-includes/widgets.php
@@ -1401,8 +1401,16 @@ function _wp_sidebars_changed() {
 	retrieve_widgets(true);
 }
 
-// look for "lost" widgets, this has to run at least on each theme change
-function retrieve_widgets($theme_changed = false) {
+/**
+ * Look for "lost" widgets, this has to run at least on each theme change.
+ *
+ * @since 2.8.0
+ *
+ * @param mixed $theme_changed Whether the theme was changed as a boolean. A value
+ *                             of 'customize' defers updates for the customizer.
+ * @return array
+ */
+function retrieve_widgets( $theme_changed = false ) {
 	global $wp_registered_sidebars, $sidebars_widgets, $wp_registered_widgets;
 
 	$registered_sidebar_keys = array_keys( $wp_registered_sidebars );
@@ -1412,7 +1420,10 @@ function retrieve_widgets($theme_changed = false) {
 	if ( is_array( $old_sidebars_widgets ) ) {
 		// time() that sidebars were stored is in $old_sidebars_widgets['time']
 		$_sidebars_widgets = $old_sidebars_widgets['data'];
-		remove_theme_mod( 'sidebars_widgets' );
+
+		if ( 'customize' === $theme_changed ) {
+			remove_theme_mod( 'sidebars_widgets' );
+		}
 
 		foreach ( $_sidebars_widgets as $sidebar => $widgets ) {
 			if ( 'wp_inactive_widgets' == $sidebar || 'orphaned_widgets' == substr( $sidebar, 0, 16 ) )
@@ -1495,7 +1506,9 @@ function retrieve_widgets($theme_changed = false) {
 	}
 
 	$sidebars_widgets['wp_inactive_widgets'] = array_merge($lost_widgets, (array) $sidebars_widgets['wp_inactive_widgets']);
-	wp_set_sidebars_widgets($sidebars_widgets);
+	if ( 'customize' === $theme_changed ) {
+		wp_set_sidebars_widgets( $sidebars_widgets );
+	}
 
 	return $sidebars_widgets;
 }