diff --git a/codex-rs/app-server/src/config_manager_service.rs b/codex-rs/app-server/src/config_manager_service.rs
index 8c8ff227e2..8509aa648d 100644
--- a/codex-rs/app-server/src/config_manager_service.rs
+++ b/codex-rs/app-server/src/config_manager_service.rs
@@ -20,7 +20,6 @@ use codex_config::ConfigLayerStackOrdering;
 use codex_config::ConfigRequirementsToml;
 use codex_config::config_toml::ConfigToml;
 use codex_config::merge_toml_values;
-use codex_config::validate_config_toml_layer;
 use codex_core::config::deserialize_config_toml_with_base;
 use codex_core::config::edit::ConfigEdit;
 use codex_core::config::edit::ConfigEditsBuilder;
@@ -294,25 +293,23 @@ impl ConfigManager {
             parsed_segments.push(segments);
         }
 
-        validate_config_toml_layer(user_config.clone(), self.codex_home()).map_err(|err| {
+        // MCP server entries may be completed by lower-precedence config layers,
+        // while feature requirements must still be checked against the user's
+        // explicit settings before the write is persisted.
+        let mut user_config_for_feature_validation = user_config.clone();
+        if let Some(table) = user_config_for_feature_validation.as_table_mut() {
+            table.remove("mcp_servers");
+        }
+        let user_config_toml = deserialize_config_toml_with_base(
+            user_config_for_feature_validation,
+            self.codex_home(),
+        )
+        .map_err(|err| {
             ConfigManagerError::write(
                 ConfigWriteErrorCode::ConfigValidationError,
                 format!("Invalid configuration: {err}"),
             )
         })?;
-
-        let mut user_config_without_mcp_servers = user_config.clone();
-        if let Some(table) = user_config_without_mcp_servers.as_table_mut() {
-            table.remove("mcp_servers");
-        }
-        let user_config_toml =
-            deserialize_config_toml_with_base(user_config_without_mcp_servers, self.codex_home())
-                .map_err(|err| {
-                ConfigManagerError::write(
-                    ConfigWriteErrorCode::ConfigValidationError,
-                    format!("Invalid configuration: {err}"),
-                )
-            })?;
         validate_feature_requirements_for_config_toml(
             &user_config_toml,
             layers.requirements().feature_requirements.as_ref(),
diff --git a/codex-rs/config/src/lib.rs b/codex-rs/config/src/lib.rs
index f857e1d7a0..1cbbbaf0a9 100644
--- a/codex-rs/config/src/lib.rs
+++ b/codex-rs/config/src/lib.rs
@@ -147,7 +147,6 @@ pub use state::ConfigLayerStackOrdering;
 pub use state::ConfigLoadOptions;
 pub use state::LoaderOverrides;
 pub use strict_config::config_error_from_ignored_toml_fields;
-pub use strict_config::validate_config_toml_layer;
 pub use thread_config::NoopThreadConfigLoader;
 pub use thread_config::RemoteThreadConfigLoader;
 pub use thread_config::SessionThreadConfig;
diff --git a/codex-rs/config/src/strict_config.rs b/codex-rs/config/src/strict_config.rs
index 0ca82203b2..8e246ab197 100644
--- a/codex-rs/config/src/strict_config.rs
+++ b/codex-rs/config/src/strict_config.rs
@@ -10,7 +10,6 @@ use crate::diagnostics::span_for_config_path;
 use crate::diagnostics::span_for_toml_key_path;
 use crate::diagnostics::text_range_from_span;
 use codex_features::is_known_feature_key;
-use codex_utils_absolute_path::AbsolutePathBufGuard;
 use serde::Deserialize;
 use serde::de::DeserializeOwned;
 use std::collections::HashMap;
@@ -60,26 +59,6 @@ pub(crate) fn config_error_from_config_toml_layer_for_source_name(
     )
 }
 
-/// Validate one config layer without requiring an MCP server fragment to
-/// contain a transport. MCP server definitions are merged recursively across
-/// config layers, so transport completeness is validated on the effective
-/// config after composition.
-pub fn validate_config_toml_layer(
-    mut value: TomlValue,
-    base_dir: &Path,
-) -> Result<(), toml::de::Error> {
-    let _guard = AbsolutePathBufGuard::new(base_dir);
-    let mcp_servers = value
-        .as_table_mut()
-        .and_then(|table| table.remove("mcp_servers"));
-
-    let _: ConfigToml = value.try_into()?;
-    if let Some(mcp_servers) = mcp_servers {
-        let _: ConfigTomlMcpServersLayer = mcp_servers_layer(mcp_servers).try_into()?;
-    }
-    Ok(())
-}
-
 /// Strictly validate one config layer while allowing MCP server fragments to
 /// receive their transport from a lower-precedence layer.
 fn config_error_from_config_toml_layer_for_source(