diff --git a/src/wp-admin/includes/plugin.php b/src/wp-admin/includes/plugin.php
index 2716bd4fef..f8ca6ea5fd 100644
--- a/src/wp-admin/includes/plugin.php
+++ b/src/wp-admin/includes/plugin.php
@@ -768,6 +768,11 @@ function deactivate_plugins( $plugins, $silent = false, $network_wide = null ) {
 			}
 		}
 
+		if ( $do_blog && wp_is_recovery_mode() ) {
+			list( $extension ) = explode( '/', $plugin );
+			wp_paused_plugins()->delete( $extension );
+		}
+
 		if ( ! $silent ) {
 			/**
 			 * Fires as a specific plugin is being deactivated.
diff --git a/src/wp-includes/theme.php b/src/wp-includes/theme.php
index e688cc66fa..eb960f8004 100644
--- a/src/wp-includes/theme.php
+++ b/src/wp-includes/theme.php
@@ -744,6 +744,12 @@ function switch_theme( $stylesheet ) {
 	$new_theme = wp_get_theme( $stylesheet );
 	$template  = $new_theme->get_template();
 
+	if ( wp_is_recovery_mode() ) {
+		$paused_themes = wp_paused_themes();
+		$paused_themes->delete( $old_theme->get_stylesheet() );
+		$paused_themes->delete( $old_theme->get_template() );
+	}
+
 	update_option( 'template', $template );
 	update_option( 'stylesheet', $stylesheet );