diff --git a/src/helper/Site_Backup_Restore.php b/src/helper/Site_Backup_Restore.php
index a287b639..4df44107 100644
--- a/src/helper/Site_Backup_Restore.php
+++ b/src/helper/Site_Backup_Restore.php
@@ -51,6 +51,9 @@ class Site_Backup_Restore {
 	// Global backup lock handle for serializing backups
 	private $global_backup_lock_handle = null;
 
+	// Per-site backup/restore lock handle (flock-based, auto-released on exit)
+	private $site_backup_lock_handle = null;
+
 	public function __construct() {
 		$this->fs = new Filesystem();
 	}
@@ -152,8 +155,6 @@ public function backup( $args, $assoc_args = [] ) {
 		$this->rclone_upload( $backup_dir );
 		$this->fs->remove( $backup_dir );
 
-		$this->fs->remove( EE_BACKUP_DIR . '/' . $this->site_data['site_url'] . '.lock' );
-
 		// Mark backup as completed and send success callback
 		$this->dash_backup_completed = true;
 		if ( $this->dash_auth_enabled ) {
@@ -173,6 +174,9 @@ public function backup( $args, $assoc_args = [] ) {
 			}
 		}
 
+		// Held until here so a same-site restore can't race the remote purges above.
+		$this->release_site_backup_lock();
+
 		// Release global backup lock (also released by shutdown handler as safety net)
 		$this->release_global_backup_lock();
 
@@ -300,7 +304,7 @@ public function restore( $args, $assoc_args = [] ) {
 		EE::log( 'Reloading site.' );
 		EE::run_command( [ 'site', 'reload', $this->site_data['site_url'] ], [], [] );
 
-		$this->fs->remove( EE_BACKUP_DIR . '/' . $this->site_data['site_url'] . '.lock' );
+		$this->release_site_backup_lock();
 
 		EE::success( 'Site restored successfully.' );
 
@@ -946,16 +950,38 @@ private function pre_backup_restore_checks() {
 
 		$lock_file = EE_BACKUP_DIR . '/' . $this->site_data['site_url'] . '.lock';
 
-		if ( $this->fs->exists( $lock_file ) ) {
+		// flock so the OS drops the lock if we die; 'e' (O_CLOEXEC) so orphaned subprocesses can't keep holding it.
+		$this->site_backup_lock_handle = fopen( $lock_file, 'c+e' );
+
+		if ( ! $this->site_backup_lock_handle ) {
+			$this->capture_error(
+				'Cannot create backup lock file',
+				self::ERROR_TYPE_FILESYSTEM,
+				5002
+			);
+			EE::error( 'Cannot create backup lock file.' );
+		}
+
+		// Non-blocking: fail fast if another backup/restore holds this site's lock.
+		if ( ! flock( $this->site_backup_lock_handle, LOCK_EX | LOCK_NB ) ) {
+			fclose( $this->site_backup_lock_handle );
+			$this->site_backup_lock_handle = null;
 			$this->capture_error(
 				'Another backup/restore process is already running for this site',
 				self::ERROR_TYPE_LOCK,
 				2003
 			);
 			EE::error( 'Another backup/restore process is running. Please wait for it to complete.' );
-		} else {
-			$this->fs->dumpFile( $lock_file, 'lock' );
 		}
+
+		// Hard kills skip shutdown functions, but the OS still drops the flock.
+		register_shutdown_function( [ $this, 'release_site_backup_lock' ] );
+
+		// Record the holder for debugging only; flock is the source of truth.
+		ftruncate( $this->site_backup_lock_handle, 0 );
+		rewind( $this->site_backup_lock_handle );
+		fwrite( $this->site_backup_lock_handle, $this->site_data['site_url'] . ' (PID: ' . getmypid() . ')' );
+		fflush( $this->site_backup_lock_handle );
 	}
 
 	private function pre_backup_check() {
@@ -987,7 +1013,7 @@ private function pre_backup_check() {
 				3001
 			);
 
-			$this->fs->remove( EE_BACKUP_DIR . '/' . $this->site_data['site_url'] . '.lock' );
+			$this->release_site_backup_lock();
 			EE::error( $error_message );
 		}
 	}
@@ -1904,8 +1930,8 @@ private function acquire_global_backup_lock() {
 			$this->fs->mkdir( EE_BACKUP_DIR );
 		}
 
-		// Open file handle (creates if doesn't exist)
-		$this->global_backup_lock_handle = fopen( $lock_file, 'c+' );
+		// 'e' (O_CLOEXEC) so orphaned subprocesses can't keep holding the lock after we die.
+		$this->global_backup_lock_handle = fopen( $lock_file, 'c+e' );
 
 		if ( ! $this->global_backup_lock_handle ) {
 			$this->capture_error(
@@ -1963,4 +1989,19 @@ public function release_global_backup_lock() {
 			EE::debug( 'Released global backup lock' );
 		}
 	}
+
+	/**
+	 * Release the per-site backup/restore lock.
+	 * Safe to call multiple times (idempotent).
+	 *
+	 * @return void
+	 */
+	public function release_site_backup_lock() {
+		if ( $this->site_backup_lock_handle ) {
+			flock( $this->site_backup_lock_handle, LOCK_UN );
+			fclose( $this->site_backup_lock_handle );
+			$this->site_backup_lock_handle = null;
+			EE::debug( 'Released per-site backup lock' );
+		}
+	}
 }
diff --git a/src/helper/class-ee-site.php b/src/helper/class-ee-site.php
index 08ad268e..b0dfd29d 100644
--- a/src/helper/class-ee-site.php
+++ b/src/helper/class-ee-site.php
@@ -2205,14 +2205,7 @@ protected function shut_down_function() {
 		$logger = \EE::get_file_logger()->withName( 'site-command' );
 		$error  = error_get_last();
 
-		// Check if the $this->site_data is set and it is array and  $this->site_data['site_url'] is set.
-		if ( isset( $this->site_data ) && is_array( $this->site_data ) && isset( $this->site_data['site_url'] ) ) {
-			// release lock if there.
-			$lock_file = EE_BACKUP_DIR . '/' . $this->site_data['site_url'] . '.lock';
-			if ( $this->fs->exists( $lock_file ) ) {
-				$this->fs->remove( $lock_file );
-			}
-		}
+		// Never unlink the per-site backup lock here: it's a flock, and a fresh inode would let a second process lock it.
 
 		if ( isset( $error ) && $error['type'] === E_ERROR ) {
 			\EE::warning( 'An Error occurred. Initiating clean-up.' );