diff --git a/codex-rs/config/src/state.rs b/codex-rs/config/src/state.rs
index 7a9a08c7b4..371e862b70 100644
--- a/codex-rs/config/src/state.rs
+++ b/codex-rs/config/src/state.rs
@@ -215,10 +215,10 @@ impl ConfigLayerStack {
 
     /// Appends warnings discovered after the raw layers have been assembled.
     ///
-    /// Invalid enum warnings are produced while deserializing the effective
-    /// config, so they are not tied to any single raw layer load. Keeping this
-    /// merge point on the stack lets callers surface them through the same
-    /// startup-warning channel used by file-level config diagnostics.
+    /// Invalid enum warnings are produced while preparing the typed effective
+    /// config, after the stack has already been constructed. Keeping this merge
+    /// point on the stack lets callers surface them through the same startup
+    /// warning channel used by file-level config diagnostics.
     pub fn with_additional_startup_warnings(mut self, warnings: Vec<String>) -> Self {
         if warnings.is_empty() {
             return self;
@@ -321,16 +321,33 @@ impl ConfigLayerStack {
     ///
     /// This is the boundary where user-editable config stays lenient for
     /// invalid enum values while consumers still receive a fully typed config.
-    /// The returned TOML value is the sanitized effective config, with invalid
-    /// enum keys removed, so callers that inspect raw values see the same shape
-    /// that was actually deserialized.
+    /// Each layer is sanitized before it is merged so a higher-precedence
+    /// invalid enum value falls back to a valid lower-precedence value.
     pub fn deserialize_effective_config_with_warnings<T>(
         &self,
     ) -> Result<(TomlValue, T, Vec<String>), toml::de::Error>
     where
         T: serde::de::DeserializeOwned,
     {
-        deserialize_with_enum_warnings(self.effective_config())
+        let mut merged = TomlValue::Table(toml::map::Map::new());
+        let mut warnings = Vec::new();
+
+        for layer in self.get_layers(
+            ConfigLayerStackOrdering::LowestPrecedenceFirst,
+            /*include_disabled*/ false,
+        ) {
+            let mut normalized_layer = TomlValue::Table(toml::map::Map::new());
+            merge_toml_values(&mut normalized_layer, &layer.config);
+            let (sanitized_layer, _typed_layer, layer_warnings) =
+                deserialize_with_enum_warnings::<T>(normalized_layer)?;
+            warnings.extend(layer_warnings);
+            merge_toml_values(&mut merged, &sanitized_layer);
+        }
+
+        let (sanitized_effective, typed_effective, effective_warnings) =
+            deserialize_with_enum_warnings::<T>(merged)?;
+        warnings.extend(effective_warnings);
+        Ok((sanitized_effective, typed_effective, warnings))
     }
 
     /// Returns field origins for the merged config-layer view.
diff --git a/codex-rs/core/src/config/config_loader_tests.rs b/codex-rs/core/src/config/config_loader_tests.rs
index 78649b18b8..07da2813ed 100644
--- a/codex-rs/core/src/config/config_loader_tests.rs
+++ b/codex-rs/core/src/config/config_loader_tests.rs
@@ -25,6 +25,7 @@ use codex_config::loader::load_config_layers_state;
 use codex_config::loader::load_requirements_toml;
 use codex_config::version_for_toml;
 use codex_exec_server::LOCAL_FS;
+use codex_protocol::config_types::SandboxMode;
 use codex_protocol::config_types::TrustLevel;
 use codex_protocol::config_types::WebSearchMode;
 use codex_protocol::models::PermissionProfile;
@@ -175,6 +176,51 @@ theme = "loudly"
     Ok(())
 }
 
+#[tokio::test]
+async fn invalid_higher_precedence_enum_falls_back_to_lower_layer() -> anyhow::Result<()> {
+    let tmp = tempdir().expect("tempdir");
+    let system_config_path = tmp.path().join("system_config.toml");
+    std::fs::write(&system_config_path, r#"sandbox_mode = "workspace-write""#)
+        .expect("write system config");
+    std::fs::write(
+        tmp.path().join(CONFIG_TOML_FILE),
+        r#"sandbox_mode = "make-it-so""#,
+    )
+    .expect("write user config");
+
+    let cwd = AbsolutePathBuf::try_from(tmp.path()).expect("cwd");
+    let layers = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        tmp.path(),
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides {
+            system_config_path: Some(system_config_path),
+            ..LoaderOverrides::without_managed_config_for_tests()
+        },
+        CloudRequirementsLoader::default(),
+        &codex_config::NoopThreadConfigLoader,
+    )
+    .await?;
+
+    let (effective_config, config_toml, enum_warnings): (TomlValue, ConfigToml, Vec<String>) =
+        layers.deserialize_effective_config_with_warnings()?;
+
+    assert_eq!(
+        (
+            effective_config.get("sandbox_mode"),
+            config_toml.sandbox_mode,
+            enum_warnings,
+        ),
+        (
+            Some(&TomlValue::String("workspace-write".to_string())),
+            Some(SandboxMode::WorkspaceWrite),
+            vec!["Ignoring invalid config value at sandbox_mode: \"make-it-so\"".to_string()],
+        )
+    );
+    Ok(())
+}
+
 #[tokio::test]
 async fn invalid_enum_values_do_not_poison_relative_path_resolution() -> anyhow::Result<()> {
     let tmp = tempdir().expect("tempdir");