diff --git a/codex-rs/core/src/mcp.rs b/codex-rs/core/src/mcp.rs
index 71571deae..abd28ec61 100644
--- a/codex-rs/core/src/mcp.rs
+++ b/codex-rs/core/src/mcp.rs
@@ -45,6 +45,12 @@ impl McpManager {
     /// runtime-only extension overlays.
     pub async fn runtime_config(&self, config: &Config) -> McpConfig {
         let mut mcp_config = config.to_mcp_config(self.plugins_manager.as_ref()).await;
+        let disabled_server_names = mcp_config
+            .configured_mcp_servers
+            .iter()
+            .filter(|(_, server)| !server.enabled)
+            .map(|(name, _)| name.clone())
+            .collect::<Vec<_>>();
         if mcp_config.apps_enabled {
             mcp_config.configured_mcp_servers.insert(
                 CODEX_APPS_MCP_SERVER_NAME.to_string(),
@@ -60,6 +66,11 @@ impl McpManager {
         }
         let contributions = self.contributions(config).await;
         Self::apply_to_configured_servers(&contributions, &mut mcp_config.configured_mcp_servers);
+        for name in disabled_server_names {
+            if let Some(server) = mcp_config.configured_mcp_servers.get_mut(&name) {
+                server.enabled = false;
+            }
+        }
         mcp_config
     }
 
diff --git a/codex-rs/ext/mcp/tests/hosted_apps_mcp.rs b/codex-rs/ext/mcp/tests/hosted_apps_mcp.rs
index bb401578f..ea1b330ca 100644
--- a/codex-rs/ext/mcp/tests/hosted_apps_mcp.rs
+++ b/codex-rs/ext/mcp/tests/hosted_apps_mcp.rs
@@ -42,6 +42,34 @@ async fn contributes_hosted_plugin_runtime_without_an_executor() -> TestResult {
     Ok(())
 }
 
+#[tokio::test]
+async fn runtime_overlay_preserves_disabled_server() -> TestResult {
+    let codex_home = tempfile::tempdir()?;
+    let config = ConfigBuilder::default()
+        .codex_home(codex_home.path().to_path_buf())
+        .fallback_cwd(Some(codex_home.path().to_path_buf()))
+        .cli_overrides(vec![
+            ("features.apps".to_string(), true.into()),
+            (
+                "mcp_servers.codex_apps.url".to_string(),
+                "https://example.com/mcp".into(),
+            ),
+            ("mcp_servers.codex_apps.enabled".to_string(), false.into()),
+        ])
+        .build()
+        .await?;
+    let auth = CodexAuth::create_dummy_chatgpt_auth_for_testing();
+    let manager = installed_manager(&config);
+
+    let servers = manager.effective_servers(&config, Some(&auth)).await;
+    let server = servers
+        .get(CODEX_APPS_MCP_SERVER_NAME)
+        .ok_or("hosted plugin runtime should remain configured")?;
+
+    assert!(!server.enabled());
+    Ok(())
+}
+
 #[tokio::test]
 async fn legacy_fallback_overwrites_reserved_config_without_an_extension() -> TestResult {
     let codex_home = tempfile::tempdir()?;