diff --git a/codex-rs/core-plugins/src/app_mcp_routing.rs b/codex-rs/core-plugins/src/app_mcp_routing.rs
new file mode 100644
index 000000000..18cacb414
--- /dev/null
+++ b/codex-rs/core-plugins/src/app_mcp_routing.rs
@@ -0,0 +1,32 @@
+use codex_app_server_protocol::AuthMode;
+use codex_plugin::AppDeclaration;
+use std::collections::HashMap;
+use std::collections::HashSet;
+
+pub fn apps_route_available(auth_mode: Option<AuthMode>) -> bool {
+    auth_mode.is_some_and(AuthMode::uses_codex_backend)
+}
+
+pub(crate) fn apply_app_mcp_routing_policy<M>(
+    apps: &mut Vec<AppDeclaration>,
+    mcp_servers: &mut HashMap<String, M>,
+    auth_mode: Option<AuthMode>,
+    plugin_active: bool,
+) {
+    if !apps_route_available(auth_mode) {
+        apps.clear();
+        return;
+    }
+
+    if plugin_active && !apps.is_empty() {
+        let app_declaration_names = apps
+            .iter()
+            .map(|app| app.name.as_str())
+            .collect::<HashSet<_>>();
+        mcp_servers.retain(|name, _| !app_declaration_names.contains(name.as_str()));
+    }
+}
+
+#[cfg(test)]
+#[path = "app_mcp_routing_tests.rs"]
+mod tests;
diff --git a/codex-rs/core-plugins/src/app_mcp_routing_tests.rs b/codex-rs/core-plugins/src/app_mcp_routing_tests.rs
new file mode 100644
index 000000000..d8050a4a6
--- /dev/null
+++ b/codex-rs/core-plugins/src/app_mcp_routing_tests.rs
@@ -0,0 +1,99 @@
+use super::*;
+use codex_plugin::AppConnectorId;
+use pretty_assertions::assert_eq;
+use std::collections::HashMap;
+
+fn app(name: &str) -> AppDeclaration {
+    AppDeclaration {
+        name: name.to_string(),
+        connector_id: AppConnectorId(format!("connector_{name}")),
+        category: None,
+    }
+}
+
+fn mcp_servers(mcp_servers: impl IntoIterator<Item = (&'static str, i32)>) -> HashMap<String, i32> {
+    mcp_servers
+        .into_iter()
+        .map(|(name, value)| (name.to_string(), value))
+        .collect::<HashMap<_, _>>()
+}
+
+fn sorted_app_names(apps: &[AppDeclaration]) -> Vec<String> {
+    let mut names = apps.iter().map(|app| app.name.clone()).collect::<Vec<_>>();
+    names.sort();
+    names
+}
+
+fn sorted_mcp_server_names(mcp_servers: &HashMap<String, i32>) -> Vec<String> {
+    let mut names = mcp_servers.keys().cloned().collect::<Vec<_>>();
+    names.sort();
+    names
+}
+
+#[test]
+fn apps_route_available_tracks_auth_mode() {
+    assert!(apps_route_available(Some(AuthMode::Chatgpt)));
+    assert!(apps_route_available(Some(AuthMode::AgentIdentity)));
+    assert!(!apps_route_available(Some(AuthMode::ApiKey)));
+    assert!(!apps_route_available(/*auth_mode*/ None));
+}
+
+#[test]
+fn app_mcp_routing_clears_apps_when_apps_route_is_unavailable() {
+    let mut apps = vec![app("linear")];
+    let mut mcp_servers = mcp_servers([("linear", 1), ("docs", 2)]);
+
+    apply_app_mcp_routing_policy(
+        &mut apps,
+        &mut mcp_servers,
+        Some(AuthMode::ApiKey),
+        /*plugin_active*/ true,
+    );
+
+    assert!(apps.is_empty());
+    assert_eq!(
+        sorted_mcp_server_names(&mcp_servers),
+        vec!["docs".to_string(), "linear".to_string()]
+    );
+}
+
+#[test]
+fn app_mcp_routing_preserves_apps_and_removes_conflicting_mcp_with_apps_route() {
+    let mut apps = vec![app("linear"), app("notion")];
+    let mut mcp_servers = mcp_servers([("linear", 1), ("docs", 2), ("notion", 3)]);
+
+    apply_app_mcp_routing_policy(
+        &mut apps,
+        &mut mcp_servers,
+        Some(AuthMode::Chatgpt),
+        /*plugin_active*/ true,
+    );
+
+    assert_eq!(
+        sorted_app_names(&apps),
+        vec!["linear".to_string(), "notion".to_string()]
+    );
+    assert_eq!(
+        sorted_mcp_server_names(&mcp_servers),
+        vec!["docs".to_string()]
+    );
+}
+
+#[test]
+fn app_mcp_routing_preserves_mcp_conflicts_when_plugin_is_inactive() {
+    let mut apps = vec![app("linear")];
+    let mut mcp_servers = mcp_servers([("linear", 1), ("docs", 2)]);
+
+    apply_app_mcp_routing_policy(
+        &mut apps,
+        &mut mcp_servers,
+        Some(AuthMode::Chatgpt),
+        /*plugin_active*/ false,
+    );
+
+    assert_eq!(sorted_app_names(&apps), vec!["linear".to_string()]);
+    assert_eq!(
+        sorted_mcp_server_names(&mcp_servers),
+        vec!["docs".to_string(), "linear".to_string()]
+    );
+}
diff --git a/codex-rs/core-plugins/src/lib.rs b/codex-rs/core-plugins/src/lib.rs
index da13b03aa..126f7b37e 100644
--- a/codex-rs/core-plugins/src/lib.rs
+++ b/codex-rs/core-plugins/src/lib.rs
@@ -1,3 +1,4 @@
+mod app_mcp_routing;
 mod discoverable;
 pub mod installed_marketplaces;
 pub mod loader;
@@ -24,6 +25,7 @@ pub const OPENAI_BUNDLED_MARKETPLACE_NAME: &str = "openai-bundled";
 pub type LoadedPlugin = codex_plugin::LoadedPlugin<codex_config::McpServerConfig>;
 pub type PluginLoadOutcome = codex_plugin::PluginLoadOutcome<codex_config::McpServerConfig>;
 
+pub use app_mcp_routing::apps_route_available;
 pub use discoverable::ToolSuggestDiscoverablePlugin;
 pub use discoverable::ToolSuggestPluginDiscoveryInput;
 pub use loader::PluginHookLoadOutcome;
diff --git a/codex-rs/core-plugins/src/loader.rs b/codex-rs/core-plugins/src/loader.rs
index ad7654765..f156f7848 100644
--- a/codex-rs/core-plugins/src/loader.rs
+++ b/codex-rs/core-plugins/src/loader.rs
@@ -1,4 +1,6 @@
 use crate::OPENAI_CURATED_MARKETPLACE_NAME;
+use crate::app_mcp_routing::apply_app_mcp_routing_policy;
+use crate::app_mcp_routing::apps_route_available;
 use crate::manifest::PluginManifestHooks;
 use crate::manifest::PluginManifestPaths;
 use crate::manifest::load_plugin_manifest;
@@ -1085,20 +1087,17 @@ pub async fn load_plugin_mcp_servers(
     auth_mode: Option<AuthMode>,
 ) -> HashMap<String, McpServerConfig> {
     let mut mcp_servers = load_declared_plugin_mcp_servers(plugin_root).await;
-    if !auth_mode.is_some_and(AuthMode::uses_codex_backend) || mcp_servers.is_empty() {
+    if !apps_route_available(auth_mode) || mcp_servers.is_empty() {
         return mcp_servers;
     }
 
-    let app_declarations = load_plugin_apps(plugin_root).await;
-    if app_declarations.is_empty() {
-        return mcp_servers;
-    }
-
-    let app_declaration_names = app_declarations
-        .iter()
-        .map(|app| app.name.as_str())
-        .collect::<HashSet<_>>();
-    mcp_servers.retain(|name, _| !app_declaration_names.contains(name.as_str()));
+    let mut app_declarations = load_plugin_apps(plugin_root).await;
+    apply_app_mcp_routing_policy(
+        &mut app_declarations,
+        &mut mcp_servers,
+        auth_mode,
+        /*plugin_active*/ true,
+    );
     mcp_servers
 }
 
diff --git a/codex-rs/core-plugins/src/manager.rs b/codex-rs/core-plugins/src/manager.rs
index b973dc729..6d2022ae5 100644
--- a/codex-rs/core-plugins/src/manager.rs
+++ b/codex-rs/core-plugins/src/manager.rs
@@ -1,5 +1,6 @@
 use super::PluginLoadOutcome;
 use crate::OPENAI_CURATED_MARKETPLACE_NAME;
+use crate::app_mcp_routing::apply_app_mcp_routing_policy;
 use crate::installed_marketplaces::installed_marketplace_roots_from_layer_stack;
 use crate::loader::PluginHookLoadOutcome;
 use crate::loader::configured_curated_plugin_ids_from_codex_home;
@@ -210,23 +211,15 @@ fn project_plugin_load_outcome_for_auth(
     outcome: PluginLoadOutcome,
     auth_mode: Option<AuthMode>,
 ) -> PluginLoadOutcome {
-    let apps_route_available = auth_mode.is_some_and(AuthMode::uses_codex_backend);
     let mut plugins = outcome.plugins().to_vec();
     for plugin in &mut plugins {
-        if apps_route_available {
-            if plugin.is_active() && !plugin.apps.is_empty() {
-                let app_declaration_names = plugin
-                    .apps
-                    .iter()
-                    .map(|app| app.name.as_str())
-                    .collect::<HashSet<_>>();
-                plugin
-                    .mcp_servers
-                    .retain(|name, _| !app_declaration_names.contains(name.as_str()));
-            }
-        } else {
-            plugin.apps.clear();
-        }
+        let plugin_active = plugin.is_active();
+        apply_app_mcp_routing_policy(
+            &mut plugin.apps,
+            &mut plugin.mcp_servers,
+            auth_mode,
+            plugin_active,
+        );
     }
     PluginLoadOutcome::from_plugins(plugins)
 }