diff --git a/features/site.feature b/features/site.feature
index 8e626db35..aea85e9a5 100644
--- a/features/site.feature
+++ b/features/site.feature
@@ -78,6 +78,42 @@ Feature: Manage sites in a multisite installation
     When I try the previous command again
     Then the return code should be 1
 
+  @skip-windows
+  Scenario: Delete a site by id and remove all prefixed tables
+    Given a WP multisite subdirectory install
+
+    When I run `wp site create --slug=first --porcelain`
+    Then STDOUT should be a number
+    And save STDOUT as {SITE_ID}
+    And I try `wp db query "CREATE TABLE wp_{SITE_ID}_custom_data (id INTEGER PRIMARY KEY);"`
+    And I run `wp site delete {SITE_ID} --yes --delete-tables-with-prefix`
+    And STDOUT should contain:
+      """
+      Success: The site at '
+      """
+
+    When I try `wp db query "CREATE TABLE wp_{SITE_ID}_custom_data (id INTEGER PRIMARY KEY);"`
+    Then STDOUT should be empty
+    And the return code should be 0
+    And I try `wp db query "DROP TABLE wp_{SITE_ID}_custom_data;"`
+    And the return code should be 0
+
+  @skip-windows
+  Scenario: Deleting a site cannot combine keep-tables with delete-tables-with-prefix
+    Given a WP multisite subdirectory install
+
+    When I run `wp site create --slug=first --porcelain`
+    Then STDOUT should be a number
+    And save STDOUT as {SITE_ID}
+
+    When I try `wp site delete {SITE_ID} --yes --keep-tables --delete-tables-with-prefix`
+    Then STDERR should be:
+      """
+      Error: The '--keep-tables' and '--delete-tables-with-prefix' flags cannot be used together.
+      """
+    And STDOUT should be empty
+    And the return code should be 1
+
   @skip-windows
   Scenario: Filter site list
     Given a WP multisite install
diff --git a/src/Site_Command.php b/src/Site_Command.php
index 5a231d7a9..472000c9e 100644
--- a/src/Site_Command.php
+++ b/src/Site_Command.php
@@ -288,6 +288,9 @@ public function empty_( $args, $assoc_args ) {
 	 * [--keep-tables]
 	 * : Delete the blog from the list, but don't drop its tables.
 	 *
+	 * [--delete-tables-with-prefix]
+	 * : Delete all tables with the site's database table prefix after deleting the site.
+	 *
 	 * ## EXAMPLES
 	 *
 	 *     $ wp site delete 123
@@ -299,11 +302,18 @@ public function delete( $args, $assoc_args ) {
 			WP_CLI::error( 'This is not a multisite installation.' );
 		}
 
+		if ( Utils\get_flag_value( $assoc_args, 'keep-tables' ) && Utils\get_flag_value( $assoc_args, 'delete-tables-with-prefix' ) ) {
+			WP_CLI::error( "The '--keep-tables' and '--delete-tables-with-prefix' flags cannot be used together." );
+		}
+
 		if ( isset( $assoc_args['slug'] ) ) {
 			$blog_id = get_id_from_blogname( $assoc_args['slug'] );
 			if ( null === $blog_id ) {
 				WP_CLI::error( sprintf( 'Could not find site with slug \'%s\'.', $assoc_args['slug'] ) );
 			}
+			if ( is_main_site( $blog_id ) ) {
+				WP_CLI::error( 'You cannot delete the root site.' );
+			}
 			$blog = get_blog_details( $blog_id );
 		} else {
 			if ( empty( $args ) ) {
@@ -327,11 +337,49 @@ public function delete( $args, $assoc_args ) {
 
 		WP_CLI::confirm( "Are you sure you want to delete the '{$site_url}' site?", $assoc_args );
 
-		wpmu_delete_blog( (int) $blog->blog_id, ! Utils\get_flag_value( $assoc_args, 'keep-tables' ) );
+		$did_delete = wpmu_delete_blog( (int) $blog->blog_id, ! Utils\get_flag_value( $assoc_args, 'keep-tables' ) );
+		if ( false === $did_delete ) {
+			WP_CLI::error( "The site at '{$site_url}' could not be deleted." );
+		}
+
+		if ( Utils\get_flag_value( $assoc_args, 'delete-tables-with-prefix' ) ) {
+			$this->drop_tables_with_prefix( (int) $blog->blog_id );
+		}
 
 		WP_CLI::success( "The site at '{$site_url}' was deleted." );
 	}
 
+	/**
+	 * Drops all database tables for a site prefix.
+	 *
+	 * @param int $blog_id Site ID.
+	 */
+	private function drop_tables_with_prefix( $blog_id ) {
+		global $wpdb;
+
+		$blog_prefix = $wpdb->get_blog_prefix( $blog_id );
+		if ( is_main_site( $blog_id ) || $blog_prefix === $wpdb->base_prefix ) {
+			WP_CLI::error( 'You cannot drop tables for the root site.' );
+		}
+
+		$prefix_like = $wpdb->esc_like( $blog_prefix ) . '%';
+		$tables      = $wpdb->get_col( $wpdb->prepare( 'SHOW TABLES LIKE %s', $prefix_like ) );
+
+		if ( empty( $tables ) ) {
+			return;
+		}
+
+		$tables = array_map(
+			static function ( $table ) {
+				return '`' . str_replace( '`', '``', $table ) . '`';
+			},
+			$tables
+		);
+
+		// phpcs:ignore WordPress.DB.PreparedSQL.NotPrepared -- Table identifiers are escaped and cannot be passed as placeholders.
+		$wpdb->query( 'DROP TABLE IF EXISTS ' . implode( ', ', $tables ) );
+	}
+
 	/**
 	 * Gets details about a site in a multisite installation.
 	 *