diff --git a/codex-rs/app-server/src/lib.rs b/codex-rs/app-server/src/lib.rs
index c6d943ae4..b92e18266 100644
--- a/codex-rs/app-server/src/lib.rs
+++ b/codex-rs/app-server/src/lib.rs
@@ -134,7 +134,7 @@ fn project_config_warning(config: &Config) -> Option<ConfigWarningNotification>
                     .disabled_reason
                     .as_ref()
                     .map(ToString::to_string)
-                    .unwrap_or_else(|| "Config folder disabled.".to_string()),
+                    .unwrap_or_else(|| "config.toml is disabled.".to_string()),
             ));
         }
     }
@@ -143,7 +143,11 @@ fn project_config_warning(config: &Config) -> Option<ConfigWarningNotification>
         return None;
     }
 
-    let mut message = "The following config folders are disabled:\n".to_string();
+    let mut message = concat!(
+        "Project config.toml files are disabled in the following folders. ",
+        "Settings in those files are ignored, but skills and exec policies still load.\n",
+    )
+    .to_string();
     for (index, (folder, reason)) in disabled_folders.iter().enumerate() {
         let display_index = index + 1;
         message.push_str(&format!("    {display_index}. {folder}\n"));
diff --git a/codex-rs/core/src/config_loader/mod.rs b/codex-rs/core/src/config_loader/mod.rs
index 6d85a7936..ae56c384e 100644
--- a/codex-rs/core/src/config_loader/mod.rs
+++ b/codex-rs/core/src/config_loader/mod.rs
@@ -512,10 +512,10 @@ impl ProjectTrustContext {
         let user_config_file = self.user_config_file.as_path().display();
         match decision.trust_level {
             Some(TrustLevel::Untrusted) => Some(format!(
-                "{trust_key} is marked as untrusted in {user_config_file}. Mark it trusted to enable project config folders."
+                "{trust_key} is marked as untrusted in {user_config_file}. To load config.toml, mark it trusted."
             )),
             _ => Some(format!(
-                "Add {trust_key} as a trusted project in {user_config_file}."
+                "To load config.toml, add {trust_key} as a trusted project in {user_config_file}."
             )),
         }
     }
@@ -526,21 +526,16 @@ fn project_layer_entry(
     dot_codex_folder: &AbsolutePathBuf,
     layer_dir: &AbsolutePathBuf,
     config: TomlValue,
+    config_toml_exists: bool,
 ) -> ConfigLayerEntry {
-    match trust_context.disabled_reason_for_dir(layer_dir) {
-        Some(reason) => ConfigLayerEntry::new_disabled(
-            ConfigLayerSource::Project {
-                dot_codex_folder: dot_codex_folder.clone(),
-            },
-            config,
-            reason,
-        ),
-        None => ConfigLayerEntry::new(
-            ConfigLayerSource::Project {
-                dot_codex_folder: dot_codex_folder.clone(),
-            },
-            config,
-        ),
+    let source = ConfigLayerSource::Project {
+        dot_codex_folder: dot_codex_folder.clone(),
+    };
+
+    if config_toml_exists && let Some(reason) = trust_context.disabled_reason_for_dir(layer_dir) {
+        ConfigLayerEntry::new_disabled(source, config, reason)
+    } else {
+        ConfigLayerEntry::new(source, config)
     }
 }
 
@@ -715,13 +710,15 @@ async fn load_project_layers(
                             &dot_codex_abs,
                             &layer_dir,
                             TomlValue::Table(toml::map::Map::new()),
+                            true,
                         ));
                         continue;
                     }
                 };
                 let config =
                     resolve_relative_paths_in_config_toml(config, dot_codex_abs.as_path())?;
-                let entry = project_layer_entry(trust_context, &dot_codex_abs, &layer_dir, config);
+                let entry =
+                    project_layer_entry(trust_context, &dot_codex_abs, &layer_dir, config, true);
                 layers.push(entry);
             }
             Err(err) => {
@@ -734,6 +731,7 @@ async fn load_project_layers(
                         &dot_codex_abs,
                         &layer_dir,
                         TomlValue::Table(toml::map::Map::new()),
+                        false,
                     ));
                 } else {
                     let config_file_display = config_file.as_path().display();
diff --git a/codex-rs/tui/src/app.rs b/codex-rs/tui/src/app.rs
index d3185adf3..bc006a292 100644
--- a/codex-rs/tui/src/app.rs
+++ b/codex-rs/tui/src/app.rs
@@ -201,7 +201,7 @@ fn emit_project_config_warnings(app_event_tx: &AppEventSender, config: &Config)
                 .disabled_reason
                 .as_ref()
                 .map(ToString::to_string)
-                .unwrap_or_else(|| "Config folder disabled.".to_string()),
+                .unwrap_or_else(|| "config.toml is disabled.".to_string()),
         ));
     }
 
@@ -209,7 +209,11 @@ fn emit_project_config_warnings(app_event_tx: &AppEventSender, config: &Config)
         return;
     }
 
-    let mut message = "The following config folders are disabled:\n".to_string();
+    let mut message = concat!(
+        "Project config.toml files are disabled in the following folders. ",
+        "Settings in those files are ignored, but skills and exec policies still load.\n",
+    )
+    .to_string();
     for (index, (folder, reason)) in disabled_folders.iter().enumerate() {
         let display_index = index + 1;
         message.push_str(&format!("    {display_index}. {folder}\n"));