diff --git a/codex-rs/app-server/tests/suite/v2/config_rpc.rs b/codex-rs/app-server/tests/suite/v2/config_rpc.rs
index 43bbed6041..809d5fa28f 100644
--- a/codex-rs/app-server/tests/suite/v2/config_rpc.rs
+++ b/codex-rs/app-server/tests/suite/v2/config_rpc.rs
@@ -856,6 +856,79 @@ model_reasoning_effort = "high"
     Ok(())
 }
 
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn config_read_respects_managed_project_root_markers() -> Result<()> {
+    let codex_home = TempDir::new()?;
+    write_config(&codex_home, "model_context_window = 16384\n")?;
+    let workspace = TempDir::new()?;
+    let ancestor_config = workspace.path().join(".codex");
+    let child = workspace.path().join("child");
+    let child_config = child.join(".codex");
+    for dir in [
+        workspace.path().join(".git"),
+        ancestor_config.clone(),
+        child_config.clone(),
+    ] {
+        std::fs::create_dir_all(dir)?;
+    }
+    std::fs::write(
+        ancestor_config.join("config.toml"),
+        "model_context_window = 32768\n",
+    )?;
+    std::fs::write(
+        child_config.join("config.toml"),
+        "model_reasoning_effort = \"high\"\n",
+    )?;
+    set_project_trust_level(codex_home.path(), workspace.path(), TrustLevel::Trusted)?;
+    let managed_path = codex_home.path().join("managed_config.toml");
+    std::fs::write(&managed_path, "project_root_markers = []\n")?;
+    let managed_path = managed_path.to_string_lossy().into_owned();
+
+    let mut app_server = TestAppServer::builder()
+        .with_codex_home(codex_home.path())
+        .without_auto_env()
+        .with_env_overrides(&[("CODEX_APP_SERVER_MANAGED_CONFIG_PATH", Some(&managed_path))])
+        .build_initialized_with_timeout(DEFAULT_READ_TIMEOUT)
+        .await?;
+    let request_id = app_server
+        .send_config_read_request(ConfigReadParams {
+            include_layers: true,
+            cwd: Some(child.to_string_lossy().into_owned()),
+        })
+        .await?;
+    let ConfigReadResponse { config, layers, .. } =
+        timeout(DEFAULT_READ_TIMEOUT, app_server.read_response(request_id)).await??;
+
+    assert_eq!(
+        (
+            config.additional.get("project_root_markers"),
+            config.model_context_window,
+            config.model_reasoning_effort,
+        ),
+        (Some(&json!([])), Some(16384), Some(ReasoningEffort::High))
+    );
+    let project_layers = layers
+        .expect("layers present")
+        .into_iter()
+        .filter_map(|layer| {
+            if let ConfigLayerSource::Project { dot_codex_folder } = layer.name {
+                Some((dot_codex_folder, layer.config, layer.disabled_reason))
+            } else {
+                None
+            }
+        })
+        .collect::<Vec<_>>();
+    assert_eq!(
+        project_layers,
+        vec![(
+            AbsolutePathBuf::try_from(child_config)?,
+            json!({"model_reasoning_effort": "high"}),
+            None,
+        )]
+    );
+    Ok(())
+}
+
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn config_read_includes_system_layer_and_overrides() -> Result<()> {
     let codex_home = TempDir::new()?;
diff --git a/codex-rs/config/src/loader/README.md b/codex-rs/config/src/loader/README.md
index 6b4129f602..9f7e869c94 100644
--- a/codex-rs/config/src/loader/README.md
+++ b/codex-rs/config/src/loader/README.md
@@ -39,6 +39,12 @@ precedence first, highest precedence last, so later layers override earlier
 layers when folded. Thread config entries supplied by `thread_config_loader` are
 inserted according to their translated `ConfigLayerSource` precedence.
 
+Project-root discovery and project trust use the applicable non-project layers,
+including legacy managed-file and MDM config at their normal precedence. The
+managed layers remain above project and session layers in the final stack.
+Executor-local reads use their own system, base-user, and legacy managed sources;
+they do not include cloud config, selected profiles, or session flags.
+
 Layers with a `disabled_reason` are still surfaced for UI, but are ignored when
 computing the effective config and origins metadata. This is what
 `ConfigLayerStack::effective_config()` implements.
@@ -77,6 +83,7 @@ Implementation is split by concern:
 
 - `state.rs`: public types (`ConfigLayerEntry`, `ConfigLayerStack`) + merge/origins convenience methods.
 - `layer_io.rs`: reading `config.toml`, managed config, and managed preferences inputs.
+- `project_discovery.rs`: shared managed-config composition for project-root and trust discovery.
 - `overrides.rs`: CLI dotted-path overrides → TOML “session flags” layer.
 - `merge.rs`: recursive TOML merge.
 - `fingerprint.rs`: stable per-layer hashing and per-key origins traversal.
diff --git a/codex-rs/config/src/loader/local.rs b/codex-rs/config/src/loader/local.rs
index de53b1e81a..2f57f552bf 100644
--- a/codex-rs/config/src/loader/local.rs
+++ b/codex-rs/config/src/loader/local.rs
@@ -3,6 +3,7 @@ use super::layer_io;
 use super::load_config_toml_for_required_layer_raw;
 use super::load_requirements_toml;
 use super::load_root_checkout_project_config;
+use super::project_discovery;
 use super::project_root_markers_from_config;
 use super::project_trust_context;
 use super::requirements_layers_from_legacy_scheme;
@@ -86,8 +87,8 @@ pub struct LocalTomlLayer<S> {
 /// config reads.
 ///
 /// Cloud, selected profiles, session flags, and thread-provided layers are not
-/// included. Project discovery uses only the executor's system and base-user
-/// configuration.
+/// included. Project discovery uses the executor's system, base-user, and
+/// legacy managed configuration.
 pub async fn load_local_config_layers(
     fs: &dyn ExecutorFileSystem,
     codex_home: &Path,
@@ -121,6 +122,13 @@ pub(super) async fn load_local_config_layers_with_overrides(
     let mut discovery_config = TomlValue::Table(toml::map::Map::new());
     merge_toml_values(&mut discovery_config, &system.toml);
     merge_toml_values(&mut discovery_config, &user.toml);
+    // Managed file and MDM values also govern the project boundary and trust.
+    // Only this snapshot is resolved; the returned local layers stay raw.
+    project_discovery::merge_managed_config_for_discovery(
+        &mut discovery_config,
+        &loaded_managed,
+        codex_home.as_path(),
+    )?;
     let project_root_markers = project_root_markers_from_config(&discovery_config)?
         .unwrap_or_else(default_project_root_markers);
     let trust_context = project_trust_context(
diff --git a/codex-rs/config/src/loader/managed_project_discovery_tests.rs b/codex-rs/config/src/loader/managed_project_discovery_tests.rs
new file mode 100644
index 0000000000..c74d8f7650
--- /dev/null
+++ b/codex-rs/config/src/loader/managed_project_discovery_tests.rs
@@ -0,0 +1,267 @@
+use crate::ConfigLayerSource;
+use crate::ConfigLayerStack;
+use crate::LoaderOverrides;
+use crate::NoopThreadConfigLoader;
+use crate::loader::LocalConfigLayers;
+use crate::loader::load_config_layers_state;
+use crate::loader::local::load_local_config_layers_with_overrides;
+use crate::loader::project_trust_key;
+use crate::loader::tests::TestFileSystem;
+use crate::merge_toml_values;
+use codex_utils_absolute_path::AbsolutePathBuf;
+use pretty_assertions::assert_eq;
+use std::path::PathBuf;
+use tempfile::TempDir;
+use toml::Value as TomlValue;
+
+struct Fixture {
+    _temp: TempDir,
+    home: PathBuf,
+    repo: AbsolutePathBuf,
+    project: AbsolutePathBuf,
+    cwd: AbsolutePathBuf,
+    managed: PathBuf,
+    overrides: LoaderOverrides,
+}
+
+impl Fixture {
+    fn new() -> anyhow::Result<Self> {
+        let temp = tempfile::tempdir()?;
+        let home = temp.path().join("home");
+        let repo = AbsolutePathBuf::from_absolute_path(temp.path().join("repo"))?;
+        let project = repo.join("project");
+        let cwd = project.join("child");
+        std::fs::create_dir_all(&home)?;
+        std::fs::create_dir_all(repo.join(".git"))?;
+        for (dir, model) in [(&repo, "ancestor"), (&project, "project"), (&cwd, "child")] {
+            std::fs::create_dir_all(dir.join(".codex"))?;
+            std::fs::write(
+                dir.join(".codex/config.toml"),
+                format!("model = \"{model}\"\n"),
+            )?;
+        }
+        std::fs::write(project.join(".company-root"), "")?;
+        let managed = temp.path().join("managed_config.toml");
+        let mut overrides = LoaderOverrides::with_managed_config_path_for_tests(managed.clone());
+        overrides.system_config_path = Some(temp.path().join("system.toml"));
+        let fixture = Self {
+            _temp: temp,
+            home,
+            repo,
+            project,
+            cwd,
+            managed,
+            overrides,
+        };
+        std::fs::write(fixture.home.join("config.toml"), fixture.trust("trusted"))?;
+        Ok(fixture)
+    }
+
+    fn trust(&self, level: &str) -> String {
+        let key = TomlValue::String(project_trust_key(self.repo.as_path()));
+        format!("[projects.{key}]\ntrust_level = \"{level}\"\n")
+    }
+
+    async fn load(&self) -> anyhow::Result<(ConfigLayerStack, LocalConfigLayers)> {
+        let canonical = load_config_layers_state(
+            &TestFileSystem,
+            &self.home,
+            Some(self.cwd.clone()),
+            &[
+                (
+                    "project_root_markers".into(),
+                    toml::Value::try_from([".git"])?,
+                ),
+                ("model".into(), TomlValue::String("session".into())),
+            ],
+            self.overrides.clone(),
+            &NoopThreadConfigLoader,
+        )
+        .await?;
+        let local = load_local_config_layers_with_overrides(
+            &TestFileSystem,
+            &self.home,
+            &self.cwd,
+            &self.overrides,
+        )
+        .await?;
+        Ok((canonical, local))
+    }
+}
+
+fn assert_discovery(
+    canonical: &ConfigLayerStack,
+    local: &LocalConfigLayers,
+    expected_dirs: &[&AbsolutePathBuf],
+    markers: &[&str],
+) -> anyhow::Result<()> {
+    let project_dirs = |sources: Vec<&ConfigLayerSource>| {
+        sources
+            .into_iter()
+            .filter_map(|source| match source {
+                ConfigLayerSource::Project { dot_codex_folder } => Some(dot_codex_folder.clone()),
+                _ => None,
+            })
+            .collect::<Vec<_>>()
+    };
+    let expected_dirs = expected_dirs
+        .iter()
+        .map(|dir| dir.join(".codex"))
+        .collect::<Vec<_>>();
+    assert_eq!(
+        (
+            project_dirs(
+                canonical
+                    .layers_low_to_high()
+                    .map(|layer| &layer.name)
+                    .collect()
+            ),
+            project_dirs(
+                local
+                    .config
+                    .layers
+                    .iter()
+                    .map(|layer| &layer.source)
+                    .collect()
+            ),
+        ),
+        (expected_dirs.clone(), expected_dirs)
+    );
+    let effective = canonical.effective_config();
+    let mut local_effective = TomlValue::Table(toml::map::Map::new());
+    for layer in &local.config.layers {
+        merge_toml_values(&mut local_effective, &layer.toml);
+    }
+    let expected_markers = TomlValue::try_from(markers)?;
+    assert_eq!(
+        (
+            effective.get("project_root_markers"),
+            local_effective.get("project_root_markers"),
+        ),
+        (Some(&expected_markers), Some(&expected_markers))
+    );
+    Ok(())
+}
+
+#[tokio::test]
+async fn managed_project_discovery_uses_file_markers_without_changing_precedence()
+-> anyhow::Result<()> {
+    let fixture = Fixture::new()?;
+    for (markers, dirs) in [
+        (
+            vec![".git"],
+            vec![&fixture.repo, &fixture.project, &fixture.cwd],
+        ),
+        (vec![], vec![&fixture.cwd]),
+        (vec![".company-root"], vec![&fixture.project, &fixture.cwd]),
+    ] {
+        let markers_toml = TomlValue::try_from(&markers)?;
+        std::fs::write(
+            &fixture.managed,
+            format!("project_root_markers = {markers_toml}\nmodel = \"managed\"\n"),
+        )?;
+        let (canonical, local) = fixture.load().await?;
+        assert_discovery(&canonical, &local, &dirs, &markers)?;
+        let managed_source = ConfigLayerSource::LegacyManagedConfigTomlFromFile {
+            file: AbsolutePathBuf::from_absolute_path(&fixture.managed)?,
+        };
+        assert_eq!(
+            (
+                canonical.effective_config().get("model").cloned(),
+                &canonical.origins()["model"].name,
+                &local.config.layers.last().expect("managed layer").source,
+            ),
+            (
+                Some(TomlValue::String("managed".into())),
+                &managed_source,
+                &managed_source,
+            )
+        );
+    }
+    Ok(())
+}
+
+#[tokio::test]
+async fn managed_project_discovery_uses_managed_project_trust() -> anyhow::Result<()> {
+    let fixture = Fixture::new()?;
+    let trust_key = project_trust_key(fixture.repo.as_path());
+    let user_config = fixture.home.join("config.toml");
+    let untrusted_reason = format!(
+        "{trust_key} is marked as untrusted in the effective configuration. To load project-local config, hooks, and exec policies, update its trust setting. If that setting is managed by your organization, contact your administrator."
+    );
+    let unknown_reason = format!(
+        "To load project-local config, hooks, and exec policies, add {trust_key} as a trusted project in {}.",
+        user_config.display()
+    );
+    for (user, managed, dirs, expected_reason) in [
+        (
+            fixture.trust("trusted"),
+            fixture.trust("untrusted"),
+            vec![],
+            Some(untrusted_reason.as_str()),
+        ),
+        (
+            fixture.trust("untrusted"),
+            fixture.trust("trusted"),
+            vec![&fixture.cwd],
+            None,
+        ),
+        (
+            String::new(),
+            String::new(),
+            vec![],
+            Some(unknown_reason.as_str()),
+        ),
+    ] {
+        std::fs::write(&user_config, user)?;
+        std::fs::write(
+            &fixture.managed,
+            format!("project_root_markers = []\n{managed}"),
+        )?;
+        let (canonical, local) = fixture.load().await?;
+        assert_discovery(&canonical, &local, &dirs, &[])?;
+        assert_eq!(
+            canonical
+                .all_layers_low_to_high()
+                .filter(|layer| matches!(layer.name, ConfigLayerSource::Project { .. }))
+                .map(|layer| layer.disabled_reason.as_deref())
+                .collect::<Vec<_>>(),
+            vec![expected_reason]
+        );
+    }
+    Ok(())
+}
+
+#[cfg(target_os = "macos")]
+#[tokio::test]
+async fn managed_project_discovery_mdm_overrides_file_markers() -> anyhow::Result<()> {
+    use base64::Engine;
+    use base64::prelude::BASE64_STANDARD;
+
+    let mut fixture = Fixture::new()?;
+    std::fs::write(&fixture.managed, "project_root_markers = [\".git\"]\n")?;
+    for (markers, dirs) in [
+        (vec![], vec![&fixture.cwd]),
+        (vec![".company-root"], vec![&fixture.project, &fixture.cwd]),
+    ] {
+        let markers_toml = TomlValue::try_from(&markers)?;
+        fixture.overrides.managed_preferences_base64 =
+            Some(BASE64_STANDARD.encode(format!("project_root_markers = {markers_toml}\n")));
+        let (canonical, local) = fixture.load().await?;
+        assert_discovery(&canonical, &local, &dirs, &markers)?;
+        assert_eq!(
+            (
+                canonical
+                    .layers_high_to_low()
+                    .next()
+                    .map(|layer| &layer.name),
+                local.config.layers.last().map(|layer| &layer.source),
+            ),
+            (
+                Some(&ConfigLayerSource::LegacyManagedConfigTomlFromMdm),
+                Some(&ConfigLayerSource::LegacyManagedConfigTomlFromMdm),
+            )
+        );
+    }
+    Ok(())
+}
diff --git a/codex-rs/config/src/loader/mod.rs b/codex-rs/config/src/loader/mod.rs
index 44058d1fee..f18c74c5ae 100644
--- a/codex-rs/config/src/loader/mod.rs
+++ b/codex-rs/config/src/loader/mod.rs
@@ -2,6 +2,7 @@ mod layer_io;
 mod local;
 #[cfg(target_os = "macos")]
 mod macos;
+mod project_discovery;
 #[cfg(test)]
 mod tests;
 
@@ -364,6 +365,13 @@ pub async fn load_config_layers_state(
         if let Some(cli_overrides_layer) = cli_overrides_layer.as_ref() {
             merge_toml_values(&mut merged_so_far, cli_overrides_layer);
         }
+        // Managed config wins over CLI config. Apply it before choosing the
+        // project root and trust, but keep its final layers above project config.
+        project_discovery::merge_managed_config_for_discovery(
+            &mut merged_so_far,
+            &loaded_config_layers,
+            codex_home,
+        )?;
 
         let project_root_markers = match project_root_markers_from_config(&merged_so_far) {
             Ok(markers) => markers.unwrap_or_else(default_project_root_markers),
@@ -1053,9 +1061,11 @@ impl ProjectTrustContext {
         let gated_features = "project-local config, hooks, and exec policies";
         let trust_key = decision.trust_key.as_str();
         let user_config_file = self.user_config_file.as_path().display();
+        // Trust may come from managed config. Keep the explicit-untrusted prefix
+        // stable because the remote TUI uses it to recognize existing decisions.
         match decision.trust_level {
             Some(TrustLevel::Untrusted) => Some(format!(
-                "{trust_key} is marked as untrusted in {user_config_file}. To load {gated_features}, mark it trusted."
+                "{trust_key} is marked as untrusted in the effective configuration. To load {gated_features}, update its trust setting. If that setting is managed by your organization, contact your administrator."
             )),
             _ => Some(format!(
                 "To load {gated_features}, add {trust_key} as a trusted project in {user_config_file}."
diff --git a/codex-rs/config/src/loader/project_discovery.rs b/codex-rs/config/src/loader/project_discovery.rs
new file mode 100644
index 0000000000..bd45090c23
--- /dev/null
+++ b/codex-rs/config/src/loader/project_discovery.rs
@@ -0,0 +1,42 @@
+//! Shared configuration composition for project-root and trust discovery.
+
+use super::layer_io::LoadedConfigLayers;
+use super::resolve_relative_paths_in_config_toml;
+use crate::merge_toml_values;
+use std::io;
+use std::path::Path;
+use toml::Value as TomlValue;
+
+/// Overlay the already-read managed sources at their normal precedence: file,
+/// then MDM. Resolve paths as the final loader does, without changing the raw
+/// layers or reading either source again.
+pub(super) fn merge_managed_config_for_discovery(
+    discovery_config: &mut TomlValue,
+    loaded: &LoadedConfigLayers,
+    codex_home: &Path,
+) -> io::Result<()> {
+    if let Some(config) = &loaded.managed_config {
+        let base_dir = config.file.as_path().parent().ok_or_else(|| {
+            io::Error::new(
+                io::ErrorKind::InvalidData,
+                format!(
+                    "Managed config file {} has no parent directory",
+                    config.file.as_path().display()
+                ),
+            )
+        })?;
+        let resolved =
+            resolve_relative_paths_in_config_toml(config.managed_config.clone(), base_dir)?;
+        merge_toml_values(discovery_config, &resolved);
+    }
+    if let Some(config) = &loaded.managed_config_from_mdm {
+        let resolved =
+            resolve_relative_paths_in_config_toml(config.managed_config.clone(), codex_home)?;
+        merge_toml_values(discovery_config, &resolved);
+    }
+    Ok(())
+}
+
+#[cfg(test)]
+#[path = "managed_project_discovery_tests.rs"]
+mod tests;
diff --git a/codex-rs/config/src/loader/tests.rs b/codex-rs/config/src/loader/tests.rs
index db1c3e0cf3..5cb1ad9af1 100644
--- a/codex-rs/config/src/loader/tests.rs
+++ b/codex-rs/config/src/loader/tests.rs
@@ -11,7 +11,7 @@ use codex_utils_path_uri::PathUri;
 use pretty_assertions::assert_eq;
 use tempfile::tempdir;
 
-struct TestFileSystem;
+pub(super) struct TestFileSystem;
 
 impl ExecutorFileSystem for TestFileSystem {
     fn canonicalize<'a>(
diff --git a/codex-rs/tui/src/config_update_tests.rs b/codex-rs/tui/src/config_update_tests.rs
index b621b52e8f..1e9f588ad6 100644
--- a/codex-rs/tui/src/config_update_tests.rs
+++ b/codex-rs/tui/src/config_update_tests.rs
@@ -1,4 +1,5 @@
 use super::*;
+use crate::history_cell::HistoryCell;
 use crate::legacy_core::config::ConfigBuilder;
 use crate::legacy_core::config::ConfigOverrides;
 use codex_app_server_client::AppServerClient;
@@ -108,6 +109,39 @@ async fn remote_project_trust_guards_thread_start_and_preserves_repository_decis
         None
     );
 
+    let response: JsonValue = app_server
+        .request_typed(ClientRequest::ConfigRead {
+            request_id: RequestId::String("untrusted-project-warning".to_string()),
+            params: ConfigReadParams {
+                include_layers: true,
+                cwd: Some(project_cwd.to_string_lossy().into_owned()),
+            },
+        })
+        .await?;
+    let reason = response["layers"]
+        .as_array()
+        .expect("config layers")
+        .iter()
+        .find(|layer| layer["name"]["type"] == "project")
+        .and_then(|layer| layer["disabledReason"].as_str())
+        .expect("explicitly untrusted project warning");
+    let warning = crate::history_cell::new_warning_event(
+        reason.replace(&project_trust_key(&project_root), "<PROJECT>"),
+    );
+    insta::assert_snapshot!(
+        warning
+            .display_lines(/*width*/ 80)
+            .iter()
+            .map(ToString::to_string)
+            .collect::<Vec<_>>()
+            .join("\n"),
+        @r"
+    ⚠ <PROJECT> is marked as untrusted in the effective configuration. To load
+      project-local config, hooks, and exec policies, update its trust setting. If
+      that setting is managed by your organization, contact your administrator.
+    "
+    );
+
     std::fs::remove_file(project_cwd.join(".codex/config.toml"))?;
     std::fs::remove_dir(project_cwd.join(".codex"))?;
     let canonical_project_cwd = PathBuf::from(project_trust_key(&project_root)).join("nested");