diff --git a/codex-rs/core/src/git_info_tests.rs b/codex-rs/core/src/git_info_tests.rs
index b13db36d1e..af62816f72 100644
--- a/codex-rs/core/src/git_info_tests.rs
+++ b/codex-rs/core/src/git_info_tests.rs
@@ -379,6 +379,50 @@ async fn test_get_has_changes_ignores_repo_fsmonitor_config() {
     );
 }
 
+#[cfg(unix)]
+#[tokio::test]
+async fn test_get_has_changes_ignores_configured_hooks_path() {
+    let temp_dir = TempDir::new().expect("Failed to create temp dir");
+    let repo_path = create_test_git_repo(&temp_dir).await;
+    let hooks_dir = repo_path.join(".git/hooks-path-test");
+    let hook_path = hooks_dir.join("post-index-change");
+    let marker_path = repo_path.join("hook-ran");
+
+    fs::create_dir_all(&hooks_dir).expect("create hook dir");
+    fs::write(
+        &hook_path,
+        format!(
+            "#!/bin/sh\nprintf ran > \"{}\"\n",
+            marker_path.to_string_lossy()
+        ),
+    )
+    .expect("write post-index-change hook");
+    let mut permissions = fs::metadata(&hook_path)
+        .expect("read hook metadata")
+        .permissions();
+    permissions.set_mode(0o755);
+    fs::set_permissions(&hook_path, permissions).expect("mark hook executable");
+
+    Command::new("git")
+        .args([
+            "config",
+            "core.hooksPath",
+            hooks_dir.to_string_lossy().as_ref(),
+        ])
+        .current_dir(&repo_path)
+        .output()
+        .await
+        .expect("configure hooks path");
+
+    fs::write(repo_path.join("test.txt"), "test content").expect("refresh tracked file");
+
+    assert_eq!(get_has_changes(&repo_path).await, Some(false));
+    assert!(
+        !marker_path.exists(),
+        "metadata collection should not invoke configured hook directories"
+    );
+}
+
 #[tokio::test]
 async fn test_get_git_working_tree_state_clean_repo() {
     let temp_dir = TempDir::new().expect("Failed to create temp dir");
diff --git a/codex-rs/git-utils/src/baseline.rs b/codex-rs/git-utils/src/baseline.rs
index c63b894049..083dd6010f 100644
--- a/codex-rs/git-utils/src/baseline.rs
+++ b/codex-rs/git-utils/src/baseline.rs
@@ -584,6 +584,51 @@ mod tests {
         assert_eq!(git_stdout(&root, &["ls-files"]), "MEMORY.md\n");
     }
 
+    #[cfg(unix)]
+    #[tokio::test]
+    async fn write_index_ignores_configured_hooks_path() {
+        use std::os::unix::fs::PermissionsExt;
+
+        let home = TempDir::new().expect("tempdir");
+        let root = home.path().join("repo");
+        let hooks_dir = root.join(".git/hooks-path-test");
+        let marker_path = root.join("hook-ran");
+        let hook_path = hooks_dir.join("post-index-change");
+
+        fs::create_dir_all(&root).expect("create root");
+        fs::write(root.join("MEMORY.md"), "baseline").expect("write memory");
+        reset_git_repository(&root).await.expect("reset repo");
+        fs::create_dir_all(&hooks_dir).expect("create hook dir");
+        fs::write(
+            &hook_path,
+            format!(
+                "#!/bin/sh\nprintf ran > \"{}\"\n",
+                marker_path.to_string_lossy()
+            ),
+        )
+        .expect("write post-index-change hook");
+        let mut permissions = fs::metadata(&hook_path)
+            .expect("read hook metadata")
+            .permissions();
+        permissions.set_mode(0o755);
+        fs::set_permissions(&hook_path, permissions).expect("mark hook executable");
+        git_stdout(
+            &root,
+            &[
+                "config",
+                "core.hooksPath",
+                hooks_dir.to_string_lossy().as_ref(),
+            ],
+        );
+
+        write_index_from_head(&root).expect("rewrite baseline index");
+
+        assert!(
+            !marker_path.exists(),
+            "baseline index writes should not invoke configured hook directories"
+        );
+    }
+
     #[tokio::test]
     async fn diff_reports_added_modified_and_deleted_files() {
         let home = TempDir::new().expect("tempdir");
diff --git a/codex-rs/git-utils/src/info.rs b/codex-rs/git-utils/src/info.rs
index 8c7c4046d4..722d556b37 100644
--- a/codex-rs/git-utils/src/info.rs
+++ b/codex-rs/git-utils/src/info.rs
@@ -40,6 +40,7 @@ pub fn get_git_repo_root(base_dir: &Path) -> Option<PathBuf> {
 
 /// Timeout for git commands to prevent freezing on large repositories
 const GIT_COMMAND_TIMEOUT: TokioDuration = TokioDuration::from_secs(5);
+const DISABLED_HOOKS_PATH: &str = if cfg!(windows) { "NUL" } else { "/dev/null" };
 
 #[derive(Serialize, Deserialize, Clone, Debug, JsonSchema, TS)]
 pub struct GitInfo {
@@ -375,6 +376,8 @@ async fn run_git_command_with_timeout(args: &[&str], cwd: &Path) -> Option<std::
     let mut command = Command::new("git");
     command
         .env("GIT_OPTIONAL_LOCKS", "0")
+        // Keep internal Git helper commands independent of configured hook directories.
+        .args(["-c", &format!("core.hooksPath={DISABLED_HOOKS_PATH}")])
         .args(["-c", "core.fsmonitor=false"])
         .args(args)
         .current_dir(cwd)
diff --git a/codex-rs/git-utils/src/operations.rs b/codex-rs/git-utils/src/operations.rs
index 921a5fd69d..f17ce209b0 100644
--- a/codex-rs/git-utils/src/operations.rs
+++ b/codex-rs/git-utils/src/operations.rs
@@ -6,6 +6,8 @@ use std::process::Command;
 
 use crate::GitToolingError;
 
+const DISABLED_HOOKS_PATH: &str = if cfg!(windows) { "NUL" } else { "/dev/null" };
+
 pub(crate) fn ensure_git_repository(path: &Path) -> Result<(), GitToolingError> {
     match run_git_for_stdout(
         path,
@@ -98,7 +100,12 @@ where
 {
     let iterator = args.into_iter();
     let (lower, upper) = iterator.size_hint();
-    let mut args_vec = Vec::with_capacity(upper.unwrap_or(lower));
+    let mut args_vec = Vec::with_capacity(upper.unwrap_or(lower) + 2);
+    // Keep internal Git helper commands independent of configured hook directories.
+    args_vec.push(OsString::from("-c"));
+    args_vec.push(OsString::from(format!(
+        "core.hooksPath={DISABLED_HOOKS_PATH}"
+    )));
     for arg in iterator {
         args_vec.push(OsString::from(arg.as_ref()));
     }