diff --git a/codex-rs/config/src/state.rs b/codex-rs/config/src/state.rs
index f4f23880e..92f36509f 100644
--- a/codex-rs/config/src/state.rs
+++ b/codex-rs/config/src/state.rs
@@ -18,6 +18,8 @@ use toml::Value as TomlValue;
 #[derive(Debug, Default, Clone)]
 pub struct LoaderOverrides {
     pub managed_config_path: Option<PathBuf>,
+    pub ignore_user_config: bool,
+    pub ignore_user_and_project_exec_policy_rules: bool,
     //TODO(gt): Add a macos_ prefix to this field and remove the target_os check.
     #[cfg(target_os = "macos")]
     pub managed_preferences_base64: Option<String>,
@@ -42,6 +44,8 @@ impl LoaderOverrides {
     pub fn with_managed_config_path_for_tests(managed_config_path: PathBuf) -> Self {
         Self {
             managed_config_path: Some(managed_config_path),
+            ignore_user_config: false,
+            ignore_user_and_project_exec_policy_rules: false,
             #[cfg(target_os = "macos")]
             managed_preferences_base64: Some(String::new()),
             macos_managed_config_requirements_base64: Some(String::new()),
@@ -157,6 +161,9 @@ pub struct ConfigLayerStack {
     /// sources. This preserves the original allow-lists so they can be
     /// surfaced via APIs.
     requirements_toml: ConfigRequirementsToml,
+
+    /// Whether execpolicy should skip `.rules` files from user and project config-layer folders.
+    ignore_user_and_project_exec_policy_rules: bool,
 }
 
 impl ConfigLayerStack {
@@ -171,9 +178,22 @@ impl ConfigLayerStack {
             user_layer_index,
             requirements,
             requirements_toml,
+            ignore_user_and_project_exec_policy_rules: false,
         })
     }
 
+    pub fn with_user_and_project_exec_policy_rules_ignored(
+        mut self,
+        ignore_user_and_project_exec_policy_rules: bool,
+    ) -> Self {
+        self.ignore_user_and_project_exec_policy_rules = ignore_user_and_project_exec_policy_rules;
+        self
+    }
+
+    pub fn ignore_user_and_project_exec_policy_rules(&self) -> bool {
+        self.ignore_user_and_project_exec_policy_rules
+    }
+
     /// Returns the raw user config layer, if any.
     ///
     /// This does not merge other config layers or apply any requirements.
@@ -211,6 +231,8 @@ impl ConfigLayerStack {
                     user_layer_index: self.user_layer_index,
                     requirements: self.requirements.clone(),
                     requirements_toml: self.requirements_toml.clone(),
+                    ignore_user_and_project_exec_policy_rules: self
+                        .ignore_user_and_project_exec_policy_rules,
                 }
             }
             None => {
@@ -232,6 +254,8 @@ impl ConfigLayerStack {
                     user_layer_index: Some(user_layer_index),
                     requirements: self.requirements.clone(),
                     requirements_toml: self.requirements_toml.clone(),
+                    ignore_user_and_project_exec_policy_rules: self
+                        .ignore_user_and_project_exec_policy_rules,
                 }
             }
         }
diff --git a/codex-rs/core/src/config/mod.rs b/codex-rs/core/src/config/mod.rs
index 7b5373f48..cd55e7e35 100644
--- a/codex-rs/core/src/config/mod.rs
+++ b/codex-rs/core/src/config/mod.rs
@@ -856,13 +856,28 @@ pub async fn load_config_as_toml_with_cli_overrides(
     codex_home: &Path,
     cwd: Option<&AbsolutePathBuf>,
     cli_overrides: Vec<(String, TomlValue)>,
+) -> std::io::Result<ConfigToml> {
+    load_config_as_toml_with_cli_and_loader_overrides(
+        codex_home,
+        cwd,
+        cli_overrides,
+        LoaderOverrides::default(),
+    )
+    .await
+}
+
+pub async fn load_config_as_toml_with_cli_and_loader_overrides(
+    codex_home: &Path,
+    cwd: Option<&AbsolutePathBuf>,
+    cli_overrides: Vec<(String, TomlValue)>,
+    loader_overrides: LoaderOverrides,
 ) -> std::io::Result<ConfigToml> {
     let config_layer_stack = load_config_layers_state(
         LOCAL_FS.as_ref(),
         codex_home,
         cwd.cloned(),
         &cli_overrides,
-        LoaderOverrides::default(),
+        loader_overrides,
         CloudRequirementsLoader::default(),
     )
     .await?;
diff --git a/codex-rs/core/src/config_loader/mod.rs b/codex-rs/core/src/config_loader/mod.rs
index 9eaeb7149..436759c72 100644
--- a/codex-rs/core/src/config_loader/mod.rs
+++ b/codex-rs/core/src/config_loader/mod.rs
@@ -128,6 +128,9 @@ pub async fn load_config_layers_state(
     overrides: LoaderOverrides,
     cloud_requirements: CloudRequirementsLoader,
 ) -> io::Result<ConfigLayerStack> {
+    let ignore_user_config = overrides.ignore_user_config;
+    let ignore_user_and_project_exec_policy_rules =
+        overrides.ignore_user_and_project_exec_policy_rules;
     let mut config_requirements_toml = ConfigRequirementsWithSources::default();
 
     if let Some(requirements) = cloud_requirements.get().await.map_err(io::Error::other)? {
@@ -189,19 +192,28 @@ pub async fn load_config_layers_state(
         .await?;
     layers.push(system_layer);
 
-    // Add a layer for $CODEX_HOME/config.toml if it exists. Note if the file
-    // exists, but is malformed, then this error should be propagated to the
-    // user.
+    // Add a layer for $CODEX_HOME/config.toml so folder-derived resources such
+    // as rules/ can still be discovered. When user config is ignored, preserve
+    // the layer metadata without reading config.toml.
     let user_file = AbsolutePathBuf::resolve_path_against_base(CONFIG_TOML_FILE, codex_home);
-    let user_layer = load_config_toml_for_required_layer(fs, &user_file, |config_toml| {
+    let user_layer = if ignore_user_config {
         ConfigLayerEntry::new(
             ConfigLayerSource::User {
                 file: user_file.clone(),
             },
-            config_toml,
+            TomlValue::Table(toml::map::Map::new()),
         )
-    })
-    .await?;
+    } else {
+        load_config_toml_for_required_layer(fs, &user_file, |config_toml| {
+            ConfigLayerEntry::new(
+                ConfigLayerSource::User {
+                    file: user_file.clone(),
+                },
+                config_toml,
+            )
+        })
+        .await?
+    };
     layers.push(user_layer);
 
     if let Some(cwd) = cwd {
@@ -312,11 +324,12 @@ pub async fn load_config_layers_state(
         ));
     }
 
-    ConfigLayerStack::new(
+    Ok(ConfigLayerStack::new(
         layers,
         config_requirements_toml.clone().try_into()?,
         config_requirements_toml.into_toml(),
-    )
+    )?
+    .with_user_and_project_exec_policy_rules_ignored(ignore_user_and_project_exec_policy_rules))
 }
 
 /// Attempts to load a config.toml file from `config_toml`.
diff --git a/codex-rs/core/src/config_loader/tests.rs b/codex-rs/core/src/config_loader/tests.rs
index a8f4eda8e..edc642ec3 100644
--- a/codex-rs/core/src/config_loader/tests.rs
+++ b/codex-rs/core/src/config_loader/tests.rs
@@ -111,6 +111,63 @@ async fn returns_config_error_for_invalid_user_config_toml() {
     assert_eq!(config_error, &expected_config_error);
 }
 
+#[tokio::test]
+async fn ignore_user_config_keeps_empty_user_layer() -> std::io::Result<()> {
+    let tmp = tempdir().expect("tempdir");
+    std::fs::write(
+        tmp.path().join(CONFIG_TOML_FILE),
+        "model = \"from-user-config\"\ninvalid = [",
+    )
+    .expect("write config");
+
+    let cwd = AbsolutePathBuf::try_from(tmp.path()).expect("cwd");
+    let layers = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        tmp.path(),
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides {
+            ignore_user_config: true,
+            ..Default::default()
+        },
+        CloudRequirementsLoader::default(),
+    )
+    .await?;
+
+    let user_layer = layers
+        .get_user_layer()
+        .expect("expected a user layer even when CODEX_HOME/config.toml is ignored");
+    assert_eq!(
+        user_layer.config,
+        TomlValue::Table(toml::map::Map::new()),
+        "expected ignored user config to preserve only layer metadata"
+    );
+    assert_eq!(layers.effective_config().get("model"), None);
+    Ok(())
+}
+
+#[tokio::test]
+async fn ignore_rules_marks_config_stack_for_exec_policy_rule_skip() -> std::io::Result<()> {
+    let tmp = tempdir().expect("tempdir");
+    let cwd = AbsolutePathBuf::try_from(tmp.path()).expect("cwd");
+
+    let layers = load_config_layers_state(
+        LOCAL_FS.as_ref(),
+        tmp.path(),
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides {
+            ignore_user_and_project_exec_policy_rules: true,
+            ..Default::default()
+        },
+        CloudRequirementsLoader::default(),
+    )
+    .await?;
+
+    assert!(layers.ignore_user_and_project_exec_policy_rules());
+    Ok(())
+}
+
 #[tokio::test]
 async fn returns_config_error_for_invalid_managed_config_toml() {
     let tmp = tempdir().expect("tempdir");
diff --git a/codex-rs/core/src/exec_policy.rs b/codex-rs/core/src/exec_policy.rs
index 8f0f076f0..dbc175deb 100644
--- a/codex-rs/core/src/exec_policy.rs
+++ b/codex-rs/core/src/exec_policy.rs
@@ -7,6 +7,7 @@ use arc_swap::ArcSwap;
 
 use crate::config_loader::ConfigLayerStack;
 use crate::config_loader::ConfigLayerStackOrdering;
+use codex_app_server_protocol::ConfigLayerSource;
 use codex_execpolicy::AmendError;
 use codex_execpolicy::Decision;
 use codex_execpolicy::Error as ExecPolicyRuleError;
@@ -505,6 +506,14 @@ pub async fn load_exec_policy(config_stack: &ConfigLayerStack) -> Result<Policy,
         ConfigLayerStackOrdering::LowestPrecedenceFirst,
         /*include_disabled*/ false,
     ) {
+        if config_stack.ignore_user_and_project_exec_policy_rules()
+            && matches!(
+                layer.name,
+                ConfigLayerSource::User { .. } | ConfigLayerSource::Project { .. }
+            )
+        {
+            continue;
+        }
         if let Some(config_folder) = layer.config_folder() {
             let policy_dir = config_folder.join(RULES_DIR_NAME);
             let layer_policy_paths = collect_policy_files(&policy_dir).await?;
diff --git a/codex-rs/core/src/exec_policy_tests.rs b/codex-rs/core/src/exec_policy_tests.rs
index 64deca6bc..c1abca5cf 100644
--- a/codex-rs/core/src/exec_policy_tests.rs
+++ b/codex-rs/core/src/exec_policy_tests.rs
@@ -6,9 +6,11 @@ use crate::config_loader::ConfigLayerStack;
 use crate::config_loader::ConfigLayerStackOrdering;
 use crate::config_loader::ConfigRequirements;
 use crate::config_loader::ConfigRequirementsToml;
+use crate::config_loader::LoaderOverrides;
 use crate::config_loader::RequirementSource;
 use crate::config_loader::Sourced;
 use codex_app_server_protocol::ConfigLayerSource;
+use codex_config::CONFIG_TOML_FILE;
 use codex_config::RequirementsExecPolicy;
 use codex_config::config_toml::ConfigToml;
 use codex_config::config_toml::ProjectConfig;
@@ -424,6 +426,73 @@ async fn ignores_policies_outside_policy_dir() {
     );
 }
 
+#[tokio::test]
+async fn ignores_policy_files_when_config_stack_disables_exec_policy_rules() {
+    let temp_dir = tempdir().expect("create temp dir");
+    let policy_dir = temp_dir.path().join(RULES_DIR_NAME);
+    fs::create_dir_all(&policy_dir).expect("create policy dir");
+    fs::write(
+        policy_dir.join("allow.rules"),
+        r#"prefix_rule(pattern=["curl"], decision="allow")"#,
+    )
+    .expect("write policy file");
+    let config_stack = config_stack_for_dot_codex_folder(temp_dir.path())
+        .with_user_and_project_exec_policy_rules_ignored(
+            /*ignore_user_and_project_exec_policy_rules*/ true,
+        );
+
+    let policy = load_exec_policy(&config_stack)
+        .await
+        .expect("policy result");
+
+    assert_eq!(
+        policy
+            .check_multiple([vec!["curl".to_string()]].iter(), &|_| Decision::Forbidden)
+            .decision,
+        Decision::Forbidden,
+    );
+}
+
+#[tokio::test]
+async fn ignore_user_project_rules_keeps_system_policy_files() {
+    let temp_dir = tempdir().expect("create temp dir");
+    let config_dir = temp_dir.path().join("system");
+    let policy_dir = config_dir.join(RULES_DIR_NAME);
+    fs::create_dir_all(&policy_dir).expect("create policy dir");
+    fs::write(
+        policy_dir.join("allow.rules"),
+        r#"prefix_rule(pattern=["curl"], decision="allow")"#,
+    )
+    .expect("write policy file");
+    let config_file =
+        AbsolutePathBuf::from_absolute_path(config_dir.join(codex_config::CONFIG_TOML_FILE))
+            .expect("absolute config file");
+    let layer = ConfigLayerEntry::new(
+        ConfigLayerSource::System { file: config_file },
+        TomlValue::Table(Default::default()),
+    );
+    let config_stack = ConfigLayerStack::new(
+        vec![layer],
+        ConfigRequirements::default(),
+        ConfigRequirementsToml::default(),
+    )
+    .expect("ConfigLayerStack")
+    .with_user_and_project_exec_policy_rules_ignored(
+        /*ignore_user_and_project_exec_policy_rules*/ true,
+    );
+
+    let policy = load_exec_policy(&config_stack)
+        .await
+        .expect("policy result");
+
+    assert_eq!(
+        policy
+            .check_multiple([vec!["curl".to_string()]].iter(), &|_| Decision::Forbidden)
+            .decision,
+        Decision::Allow,
+    );
+}
+
 #[tokio::test]
 async fn ignores_rules_from_untrusted_project_layers() -> anyhow::Result<()> {
     let project_dir = tempdir()?;
@@ -575,6 +644,45 @@ fn commands_for_exec_policy_falls_back_for_whitespace_shell_script() {
     assert_eq!(commands_for_exec_policy(&command), (vec![command], false));
 }
 
+#[tokio::test]
+async fn ignore_user_config_keeps_user_policy_files() -> std::io::Result<()> {
+    let temp = tempdir()?;
+    let codex_home = temp.path().join("home_ignore_user_config");
+    let rules_dir = codex_home.join(RULES_DIR_NAME);
+    fs::create_dir_all(&rules_dir)?;
+    fs::write(
+        codex_home.join(CONFIG_TOML_FILE),
+        "model = \"from-user-config\"\ninvalid = [",
+    )?;
+    fs::write(
+        rules_dir.join("deny-curl.rules"),
+        r#"prefix_rule(pattern=["curl"], decision="forbidden")"#,
+    )?;
+
+    let config = ConfigBuilder::default()
+        .codex_home(codex_home)
+        .fallback_cwd(Some(temp.path().to_path_buf()))
+        .loader_overrides(LoaderOverrides {
+            ignore_user_config: true,
+            ..Default::default()
+        })
+        .build()
+        .await?;
+
+    let policy = load_exec_policy(&config.config_layer_stack)
+        .await
+        .map_err(std::io::Error::other)?;
+
+    assert_eq!(
+        policy
+            .check_multiple([vec!["curl".to_string()]].iter(), &|_| Decision::Allow)
+            .decision,
+        Decision::Forbidden,
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn evaluates_heredoc_script_against_prefix_rules() {
     let command = vec![
diff --git a/codex-rs/exec/src/cli.rs b/codex-rs/exec/src/cli.rs
index 0225dc176..4d34e7f36 100644
--- a/codex-rs/exec/src/cli.rs
+++ b/codex-rs/exec/src/cli.rs
@@ -78,6 +78,14 @@ pub struct Cli {
     #[arg(long = "ephemeral", global = true, default_value_t = false)]
     pub ephemeral: bool,
 
+    /// Do not load `$CODEX_HOME/config.toml`; auth still uses `CODEX_HOME`.
+    #[arg(long = "ignore-user-config", global = true, default_value_t = false)]
+    pub ignore_user_config: bool,
+
+    /// Do not load user or project execpolicy `.rules` files.
+    #[arg(long = "ignore-rules", global = true, default_value_t = false)]
+    pub ignore_rules: bool,
+
     /// Path to a JSON Schema file describing the model's final response shape.
     #[arg(long = "output-schema", value_name = "FILE")]
     pub output_schema: Option<PathBuf>,
diff --git a/codex-rs/exec/src/cli_tests.rs b/codex-rs/exec/src/cli_tests.rs
index bf4884f24..dfa202884 100644
--- a/codex-rs/exec/src/cli_tests.rs
+++ b/codex-rs/exec/src/cli_tests.rs
@@ -14,10 +14,14 @@ fn resume_parses_prompt_after_global_flags() {
         "--dangerously-bypass-approvals-and-sandbox",
         "--skip-git-repo-check",
         "--ephemeral",
+        "--ignore-user-config",
+        "--ignore-rules",
         PROMPT,
     ]);
 
     assert!(cli.ephemeral);
+    assert!(cli.ignore_user_config);
+    assert!(cli.ignore_rules);
     let Some(Command::Resume(args)) = cli.command else {
         panic!("expected resume command");
     };
@@ -53,3 +57,16 @@ fn resume_accepts_output_last_message_flag_after_subcommand() {
     assert_eq!(args.session_id.as_deref(), Some("session-123"));
     assert_eq!(args.prompt.as_deref(), Some(PROMPT));
 }
+
+#[test]
+fn parses_config_isolation_flags() {
+    let cli = Cli::parse_from([
+        "codex-exec",
+        "--ignore-user-config",
+        "--ignore-rules",
+        "summarize",
+    ]);
+
+    assert!(cli.ignore_user_config);
+    assert!(cli.ignore_rules);
+}
diff --git a/codex-rs/exec/src/lib.rs b/codex-rs/exec/src/lib.rs
index 35f2ae49a..6093e6e19 100644
--- a/codex-rs/exec/src/lib.rs
+++ b/codex-rs/exec/src/lib.rs
@@ -56,7 +56,7 @@ use codex_core::config::Config;
 use codex_core::config::ConfigBuilder;
 use codex_core::config::ConfigOverrides;
 use codex_core::config::find_codex_home;
-use codex_core::config::load_config_as_toml_with_cli_overrides;
+use codex_core::config::load_config_as_toml_with_cli_and_loader_overrides;
 use codex_core::config::resolve_oss_provider;
 use codex_core::config_loader::ConfigLoadError;
 use codex_core::config_loader::LoaderOverrides;
@@ -230,6 +230,8 @@ pub async fn run_main(cli: Cli, arg0_paths: Arg0DispatchPaths) -> anyhow::Result
         skip_git_repo_check,
         add_dir,
         ephemeral,
+        ignore_user_config,
+        ignore_rules,
         color,
         last_message_file,
         json: json_mode,
@@ -297,10 +299,17 @@ pub async fn run_main(cli: Cli, arg0_paths: Arg0DispatchPaths) -> anyhow::Result
     };
 
     #[allow(clippy::print_stderr)]
-    let config_toml = match load_config_as_toml_with_cli_overrides(
+    let loader_overrides = LoaderOverrides {
+        ignore_user_config,
+        ignore_user_and_project_exec_policy_rules: ignore_rules,
+        ..Default::default()
+    };
+
+    let config_toml = match load_config_as_toml_with_cli_and_loader_overrides(
         &codex_home,
         Some(&config_cwd),
         cli_kv_overrides.clone(),
+        loader_overrides.clone(),
     )
     .await
     {
@@ -334,7 +343,7 @@ pub async fn run_main(cli: Cli, arg0_paths: Arg0DispatchPaths) -> anyhow::Result
         chatgpt_base_url,
     );
     let run_cli_overrides = cli_kv_overrides.clone();
-    let run_loader_overrides = LoaderOverrides::default();
+    let run_loader_overrides = loader_overrides.clone();
     let run_cloud_requirements = cloud_requirements.clone();
 
     let model_provider = if oss {
@@ -399,6 +408,7 @@ pub async fn run_main(cli: Cli, arg0_paths: Arg0DispatchPaths) -> anyhow::Result
     let config = ConfigBuilder::default()
         .cli_overrides(cli_kv_overrides)
         .harness_overrides(overrides)
+        .loader_overrides(loader_overrides)
         .cloud_requirements(cloud_requirements)
         .build()
         .await?;