diff --git a/codex-rs/config/src/loader/mod.rs b/codex-rs/config/src/loader/mod.rs
index 49df306abb..bcd32f0159 100644
--- a/codex-rs/config/src/loader/mod.rs
+++ b/codex-rs/config/src/loader/mod.rs
@@ -906,6 +906,13 @@ fn project_ignored_config_keys_warning(
     )
 }
 
+fn malformed_disabled_project_config_warning(config_path: &Path, err: &toml::de::Error) -> String {
+    format!(
+        "Ignored malformed project-local config in {} because this project is not trusted: {err}",
+        config_path.display()
+    )
+}
+
 async fn project_trust_context(
     fs: &dyn ExecutorFileSystem,
     merged_config: &TomlValue,
@@ -1182,6 +1189,10 @@ async fn load_project_layers(
                                 ),
                             ));
                         }
+                        startup_warnings.push(malformed_disabled_project_config_warning(
+                            config_file.as_path(),
+                            &e,
+                        ));
                         layers.push(project_layer_entry(
                             &dot_codex_abs,
                             TomlValue::Table(toml::map::Map::new()),
@@ -1208,6 +1219,7 @@ async fn load_project_layers(
                     config,
                     hooks_config_folder_override.as_ref(),
                     decision.is_trusted(),
+                    &mut startup_warnings,
                 )
                 .await?;
                 if disabled_reason.is_none() && !ignored_project_config_keys.is_empty() {
@@ -1234,6 +1246,7 @@ async fn load_project_layers(
                         TomlValue::Table(toml::map::Map::new()),
                         hooks_config_folder_override.as_ref(),
                         decision.is_trusted(),
+                        &mut startup_warnings,
                     )
                     .await?;
                     layers.push(project_layer_entry(
@@ -1266,6 +1279,7 @@ async fn merge_root_checkout_project_hooks(
     mut config: TomlValue,
     hooks_config_folder_override: Option<&AbsolutePathBuf>,
     is_trusted: bool,
+    startup_warnings: &mut Vec<String>,
 ) -> io::Result<TomlValue> {
     let Some(hooks_config_folder) = hooks_config_folder_override else {
         return Ok(config);
@@ -1288,6 +1302,10 @@ async fn merge_root_checkout_project_hooks(
                             ),
                         ));
                     }
+                    startup_warnings.push(malformed_disabled_project_config_warning(
+                        hooks_config_file.as_path(),
+                        &err,
+                    ));
                     TomlValue::Table(toml::map::Map::new())
                 }
             };
diff --git a/codex-rs/core/src/config/config_loader_tests.rs b/codex-rs/core/src/config/config_loader_tests.rs
index 760b1f3fc5..f261ff3ce5 100644
--- a/codex-rs/core/src/config/config_loader_tests.rs
+++ b/codex-rs/core/src/config/config_loader_tests.rs
@@ -1830,6 +1830,76 @@ async fn linked_worktree_project_layers_use_root_repo_hooks_without_worktree_con
     Ok(())
 }
 
+#[tokio::test]
+async fn malformed_linked_worktree_root_hooks_config_warns_when_project_is_disabled()
+-> std::io::Result<()> {
+    let tmp = tempdir()?;
+    let repo_root = tmp.path().join("repo");
+    let root_dot_codex = repo_root.join(".codex");
+    let worktree_root = tmp.path().join("worktree");
+
+    tokio::fs::create_dir_all(&root_dot_codex).await?;
+    tokio::fs::create_dir_all(worktree_root.join(".codex")).await?;
+    write_linked_worktree_pointer(&repo_root, &worktree_root).await?;
+    let root_config_path = root_dot_codex.join(CONFIG_TOML_FILE);
+    tokio::fs::write(
+        &root_config_path,
+        r#"[hooks
+"#,
+    )
+    .await?;
+
+    let codex_home = tmp.path().join("home");
+    tokio::fs::create_dir_all(&codex_home).await?;
+    make_config_for_test(
+        &codex_home,
+        &repo_root,
+        TrustLevel::Untrusted,
+        /*project_root_markers*/ None,
+    )
+    .await?;
+
+    let cwd = AbsolutePathBuf::from_absolute_path(&worktree_root)?;
+    let layers = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        &codex_home,
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+        CloudRequirementsLoader::default(),
+        &codex_config::NoopThreadConfigLoader,
+    )
+    .await?;
+
+    let project_layers: Vec<_> = layers
+        .get_layers(
+            ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            /*include_disabled*/ true,
+        )
+        .into_iter()
+        .filter(|layer| matches!(layer.name, ConfigLayerSource::Project { .. }))
+        .collect();
+    assert_eq!(project_layers.len(), 1);
+    assert!(
+        project_layers[0].disabled_reason.is_some(),
+        "expected malformed linked worktree root hooks config layer to be disabled"
+    );
+    assert_eq!(project_hook_command(project_layers[0]), None);
+    let warnings = layers
+        .startup_warnings()
+        .expect("expected malformed linked worktree root hooks config warning");
+    assert_eq!(warnings.len(), 1);
+    assert!(
+        warnings[0].contains(&format!(
+            "Ignored malformed project-local config in {} because this project is not trusted:",
+            root_config_path.display()
+        )),
+        "warning should explain that malformed linked worktree hooks config was ignored"
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn nested_project_root_markers_do_not_redirect_regular_repo_hooks() -> std::io::Result<()> {
     let tmp = tempdir()?;
@@ -2328,6 +2398,170 @@ profile = "ignored"
     Ok(())
 }
 
+#[tokio::test]
+async fn malformed_project_config_warns_when_disabled_and_fails_when_trusted() -> std::io::Result<()>
+{
+    let tmp = tempdir()?;
+    let project_root = tmp.path().join("project");
+    let nested = project_root.join("child");
+    let dot_codex = nested.join(".codex");
+    tokio::fs::create_dir_all(&dot_codex).await?;
+    let project_config_path = dot_codex.join(CONFIG_TOML_FILE);
+    tokio::fs::write(
+        &project_config_path,
+        r#"foo = "child
+"#,
+    )
+    .await?;
+
+    let cwd = AbsolutePathBuf::from_absolute_path(&nested)?;
+
+    let codex_home_untrusted = tmp.path().join("home_untrusted_malformed");
+    tokio::fs::create_dir_all(&codex_home_untrusted).await?;
+    make_config_for_test(
+        &codex_home_untrusted,
+        &project_root,
+        TrustLevel::Untrusted,
+        /*project_root_markers*/ None,
+    )
+    .await?;
+    let untrusted_config_path = codex_home_untrusted.join(CONFIG_TOML_FILE);
+    let untrusted_config_contents = tokio::fs::read_to_string(&untrusted_config_path).await?;
+    tokio::fs::write(
+        &untrusted_config_path,
+        format!(
+            r#"foo = "user"
+{untrusted_config_contents}"#
+        ),
+    )
+    .await?;
+
+    let layers_untrusted = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        &codex_home_untrusted,
+        Some(cwd.clone()),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+        CloudRequirementsLoader::default(),
+        &codex_config::NoopThreadConfigLoader,
+    )
+    .await?;
+    let project_layers_untrusted: Vec<_> = layers_untrusted
+        .get_layers(
+            ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            /*include_disabled*/ true,
+        )
+        .into_iter()
+        .filter(|layer| matches!(layer.name, ConfigLayerSource::Project { .. }))
+        .collect();
+    assert_eq!(project_layers_untrusted.len(), 1);
+    assert!(
+        project_layers_untrusted[0].disabled_reason.is_some(),
+        "expected malformed untrusted project layer to be disabled"
+    );
+    assert_eq!(
+        project_layers_untrusted[0].config,
+        TomlValue::Table(toml::map::Map::new())
+    );
+    assert_eq!(
+        layers_untrusted.effective_config().get("foo"),
+        Some(&TomlValue::String("user".to_string()))
+    );
+    let untrusted_warnings = layers_untrusted
+        .startup_warnings()
+        .expect("expected malformed project config warning");
+    assert_eq!(untrusted_warnings.len(), 1);
+    assert!(
+        untrusted_warnings[0].contains(&format!(
+            "Ignored malformed project-local config in {} because this project is not trusted:",
+            project_config_path.display()
+        )),
+        "warning should explain that malformed untrusted project config was ignored"
+    );
+
+    let codex_home_unknown = tmp.path().join("home_unknown_malformed");
+    tokio::fs::create_dir_all(&codex_home_unknown).await?;
+    tokio::fs::write(
+        codex_home_unknown.join(CONFIG_TOML_FILE),
+        r#"foo = "user"
+"#,
+    )
+    .await?;
+
+    let layers_unknown = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        &codex_home_unknown,
+        Some(cwd.clone()),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+        CloudRequirementsLoader::default(),
+        &codex_config::NoopThreadConfigLoader,
+    )
+    .await?;
+    let project_layers_unknown: Vec<_> = layers_unknown
+        .get_layers(
+            ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            /*include_disabled*/ true,
+        )
+        .into_iter()
+        .filter(|layer| matches!(layer.name, ConfigLayerSource::Project { .. }))
+        .collect();
+    assert_eq!(project_layers_unknown.len(), 1);
+    assert!(
+        project_layers_unknown[0].disabled_reason.is_some(),
+        "expected malformed unknown-trust project layer to be disabled"
+    );
+    assert_eq!(
+        project_layers_unknown[0].config,
+        TomlValue::Table(toml::map::Map::new())
+    );
+    assert_eq!(
+        layers_unknown.effective_config().get("foo"),
+        Some(&TomlValue::String("user".to_string()))
+    );
+    let unknown_warnings = layers_unknown
+        .startup_warnings()
+        .expect("expected malformed project config warning");
+    assert_eq!(unknown_warnings.len(), 1);
+    assert!(
+        unknown_warnings[0].contains(&format!(
+            "Ignored malformed project-local config in {} because this project is not trusted:",
+            project_config_path.display()
+        )),
+        "warning should explain that malformed unknown-trust project config was ignored"
+    );
+
+    let codex_home_trusted = tmp.path().join("home_trusted_malformed");
+    tokio::fs::create_dir_all(&codex_home_trusted).await?;
+    make_config_for_test(
+        &codex_home_trusted,
+        &project_root,
+        TrustLevel::Trusted,
+        /*project_root_markers*/ None,
+    )
+    .await?;
+
+    let err = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        &codex_home_trusted,
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+        CloudRequirementsLoader::default(),
+        &codex_config::NoopThreadConfigLoader,
+    )
+    .await
+    .expect_err("trusted malformed project config should fail");
+    assert_eq!(err.kind(), std::io::ErrorKind::InvalidData);
+    assert!(
+        err.to_string()
+            .contains("Error parsing project config file"),
+        "trusted project config parse errors should still fail loudly"
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn project_layer_ignores_unsupported_config_keys() -> std::io::Result<()> {
     let tmp = tempdir()?;