diff --git a/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart b/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart
index 4fce8b75..2edb221f 100644
--- a/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart
+++ b/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart
@@ -210,9 +210,12 @@ Future<CallToolResult> runCommandInRoot(
   }
   commandWithPaths.addAll(paths);
 
+  final workingDir = fileSystem.directory(projectRoot.path);
+  await workingDir.create(recursive: true);
+
   final result = await processManager.run(
     commandWithPaths,
-    workingDirectory: projectRoot.path,
+    workingDirectory: workingDir.path,
     runInShell: true,
   );
 
diff --git a/pkgs/dart_mcp_server/test/utils/cli_utils_test.dart b/pkgs/dart_mcp_server/test/utils/cli_utils_test.dart
index 36b97e11..9a5fa1ce 100644
--- a/pkgs/dart_mcp_server/test/utils/cli_utils_test.dart
+++ b/pkgs/dart_mcp_server/test/utils/cli_utils_test.dart
@@ -54,6 +54,7 @@ void main() {
     test(
       'can run commands with roots that are subdirectories of known roots',
       () async {
+        expect(fileSystem.directory('/bar/baz').existsSync(), false);
         final result = await runCommandInRoots(
           CallToolRequest(
             name: 'foo',
@@ -76,6 +77,7 @@ void main() {
             workingDirectory: '/bar/baz/',
           )),
         ]);
+        expect(fileSystem.directory('/bar/baz').existsSync(), true);
       },
     );
   });