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 7ae8ae02..80926e5a 100644
--- a/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart
+++ b/pkgs/dart_mcp_server/lib/src/utils/cli_utils.dart
@@ -26,13 +26,16 @@ enum ProjectKind {
   unknown,
 }
 
-/// Infers the [ProjectKind] of a given [Root].
+/// Infers the [ProjectKind] of a given project at [rootUri].
 ///
 /// Currently, this is done by checking for the existence of a `pubspec.yaml`
 /// file and whether it contains a Flutter SDK dependency.
-Future<ProjectKind> inferProjectKind(Root root, FileSystem fileSystem) async {
+Future<ProjectKind> inferProjectKind(
+  String rootUri,
+  FileSystem fileSystem,
+) async {
   final pubspecFile = fileSystem
-      .directory(Uri.parse(root.uri))
+      .directory(Uri.parse(rootUri))
       .childFile('pubspec.yaml');
   if (!await pubspecFile.exists()) {
     return ProjectKind.unknown;
@@ -73,7 +76,7 @@ Future<ProjectKind> inferProjectKind(Root root, FileSystem fileSystem) async {
 /// root's 'paths'.
 Future<CallToolResult> runCommandInRoots(
   CallToolRequest request, {
-  FutureOr<String> Function(Root, FileSystem, Sdk) commandForRoot =
+  FutureOr<String> Function(String, FileSystem, Sdk) commandForRoot =
       defaultCommandForRoot,
   List<String> arguments = const [],
   required String commandDescription,
@@ -138,7 +141,7 @@ Future<CallToolResult> runCommandInRoots(
 Future<CallToolResult> runCommandInRoot(
   CallToolRequest request, {
   Map<String, Object?>? rootConfig,
-  FutureOr<String> Function(Root, FileSystem, Sdk) commandForRoot =
+  FutureOr<String> Function(String, FileSystem, Sdk) commandForRoot =
       defaultCommandForRoot,
   List<String> arguments = const [],
   required String commandDescription,
@@ -192,7 +195,7 @@ Future<CallToolResult> runCommandInRoot(
   final projectRoot = fileSystem.directory(rootUri);
 
   final commandWithPaths = <String>[
-    await commandForRoot(root, fileSystem, sdk),
+    await commandForRoot(rootUriString, fileSystem, sdk),
     ...arguments,
   ];
   final paths =
@@ -247,17 +250,17 @@ Future<CallToolResult> runCommandInRoot(
 ///
 /// Throws an [ArgumentError] if there is no pubspec.
 Future<String> defaultCommandForRoot(
-  Root root,
+  String rootUri,
   FileSystem fileSystem,
   Sdk sdk,
-) async => switch (await inferProjectKind(root, fileSystem)) {
+) async => switch (await inferProjectKind(rootUri, fileSystem)) {
   ProjectKind.dart => sdk.dartExecutablePath,
   ProjectKind.flutter => sdk.flutterExecutablePath,
   ProjectKind.unknown =>
     throw ArgumentError.value(
-      root.uri,
-      'root.uri',
-      'Unknown project kind at root ${root.uri}. All projects must have a '
+      rootUri,
+      'rootUri',
+      'Unknown project kind at root $rootUri. All projects must have a '
           'pubspec.',
     ),
 };
diff --git a/pkgs/dart_mcp_server/test/tools/pub_test.dart b/pkgs/dart_mcp_server/test/tools/pub_test.dart
index 693b99e6..19ba59b7 100644
--- a/pkgs/dart_mcp_server/test/tools/pub_test.dart
+++ b/pkgs/dart_mcp_server/test/tools/pub_test.dart
@@ -141,6 +141,33 @@ void main() {
           ]);
         });
 
+        test('in a subdir of an a root', () async {
+          fileSystem.file(p.join(fakeAppPath, 'subdir', 'pubspec.yaml'))
+            ..createSync(recursive: true)
+            ..writeAsStringSync(
+              appKind == 'flutter' ? flutterPubspec : dartPubspec,
+            );
+          final request = CallToolRequest(
+            name: dartPubTool.name,
+            arguments: {
+              ParameterNames.command: 'get',
+              ParameterNames.roots: [
+                {ParameterNames.root: p.join(testRoot.uri, 'subdir')},
+              ],
+            },
+          );
+          final result = await testHarness.callToolWithRetry(request);
+
+          // Verify the command was sent to the process manager without error.
+          expect(result.isError, isNot(true));
+          expect(testProcessManager.commandsRan, [
+            equalsCommand((
+              command: [endsWith(appKind), 'pub', 'get'],
+              workingDirectory: p.join(fakeAppPath, 'subdir'),
+            )),
+          ]);
+        });
+
         group('returns error', () {
           test('for missing command', () async {
             final request = CallToolRequest(name: dartPubTool.name);