diff --git a/codex-rs/core/tests/suite/workspace_roots.rs b/codex-rs/core/tests/suite/workspace_roots.rs
index e066897b4c..8170a8674c 100644
--- a/codex-rs/core/tests/suite/workspace_roots.rs
+++ b/codex-rs/core/tests/suite/workspace_roots.rs
@@ -1,5 +1,6 @@
 use anyhow::Context;
 use anyhow::Result;
+use codex_exec_server::CreateDirectoryOptions;
 use codex_exec_server::RemoveOptions;
 use codex_features::Feature;
 use codex_protocol::models::PermissionProfile;
@@ -187,6 +188,96 @@ async fn workspace_roots_allow_file_and_command_writes() -> Result<()> {
     remove_files(&test, &[&patch_path, &command_path]).await
 }
 
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn workspace_roots_allow_patches_but_protect_metadata_directories() -> Result<()> {
+    const PATCH_CONTENTS: &str = "workspace root patch access";
+    const PROTECTED_METADATA_DIRECTORIES: [&str; 3] = [".git", ".agents", ".codex"];
+
+    skip_if_wine_exec!(
+        Ok(()),
+        "Wine does not emulate Windows restricted-token and ACL sandbox semantics"
+    );
+
+    let server = start_mock_server().await;
+    let test = workspace_roots_test(&server).await?;
+    let cwd = PathUri::from_abs_path(&test.config.cwd);
+    let allowed_path = cwd.join("workspace-root-allowed-patch.txt")?;
+    for directory in PROTECTED_METADATA_DIRECTORIES {
+        test.fs()
+            .create_directory(
+                &cwd.join(directory)?,
+                CreateDirectoryOptions { recursive: true },
+                /*sandbox*/ None,
+            )
+            .await?;
+    }
+
+    let allowed_patch = format!(
+        "*** Begin Patch\n*** Add File: workspace-root-allowed-patch.txt\n+{PATCH_CONTENTS}\n*** End Patch\n"
+    );
+    let mut patch_calls = vec![
+        ev_response_created("resp-1"),
+        ev_apply_patch_custom_tool_call(PATCH_CALL_ID, &allowed_patch),
+    ];
+    for directory in PROTECTED_METADATA_DIRECTORIES {
+        let call_id = format!("workspace-root-protected-{directory}");
+        let patch = format!(
+            "*** Begin Patch\n*** Add File: {directory}/protected.txt\n+metadata write\n*** End Patch\n"
+        );
+        patch_calls.push(ev_apply_patch_custom_tool_call(&call_id, &patch));
+    }
+    patch_calls.push(ev_completed("resp-1"));
+    let response_mock = mount_sse_sequence(
+        &server,
+        vec![
+            sse(patch_calls),
+            sse(vec![
+                ev_response_created("resp-2"),
+                ev_assistant_message("msg-1", "done"),
+                ev_completed("resp-2"),
+            ]),
+        ],
+    )
+    .await;
+
+    submit_workspace_turn(&test, "patch the workspace and protected metadata").await?;
+
+    let request = response_mock
+        .last_request()
+        .context("model should receive every workspace-root patch result")?;
+    let (_, patch_success) = request
+        .custom_tool_call_output_content_and_success(PATCH_CALL_ID)
+        .context("workspace patch result should be present")?;
+    assert_ne!(patch_success, Some(false));
+    assert_eq!(
+        read_file(&test, &allowed_path).await?,
+        format!("{PATCH_CONTENTS}\n")
+    );
+
+    for directory in PROTECTED_METADATA_DIRECTORIES {
+        let call_id = format!("workspace-root-protected-{directory}");
+        let (output, success) = request
+            .custom_tool_call_output_content_and_success(&call_id)
+            .with_context(|| format!("{directory} patch result should be present"))?;
+        assert_ne!(success, Some(true));
+        assert!(
+            output
+                .as_deref()
+                .is_some_and(|output| output.contains("outside of the project")),
+            "{directory} patch should be denied, got {output:?}"
+        );
+        let protected_path = cwd.join(directory)?.join("protected.txt")?;
+        let error = test
+            .fs()
+            .get_metadata(&protected_path, /*sandbox*/ None)
+            .await
+            .expect_err("protected metadata file should not be created");
+        assert_eq!(error.kind(), std::io::ErrorKind::NotFound);
+    }
+
+    remove_files(&test, &[&allowed_path]).await
+}
+
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn workspace_roots_deny_file_and_command_writes_outside_roots() -> Result<()> {
     const PATCH_CONTENTS: &str = "outside workspace root patch";