diff --git a/codex-rs/core/src/config_loader/mod.rs b/codex-rs/core/src/config_loader/mod.rs
index eba89fdb3d..838db0d5ff 100644
--- a/codex-rs/core/src/config_loader/mod.rs
+++ b/codex-rs/core/src/config_loader/mod.rs
@@ -25,6 +25,7 @@ use codex_protocol::config_types::TrustLevel;
 use codex_protocol::protocol::AskForApproval;
 use codex_utils_absolute_path::AbsolutePathBuf;
 use codex_utils_absolute_path::AbsolutePathBufGuard;
+use dunce::canonicalize as normalize_path;
 use serde::Deserialize;
 use std::io;
 use std::path::Path;
@@ -236,6 +237,7 @@ pub async fn load_config_layers_state(
             &cwd,
             &project_trust_context.project_root,
             &project_trust_context,
+            codex_home,
         )
         .await?;
         layers.extend(project_layers);
@@ -671,7 +673,11 @@ async fn load_project_layers(
     cwd: &AbsolutePathBuf,
     project_root: &AbsolutePathBuf,
     trust_context: &ProjectTrustContext,
+    codex_home: &Path,
 ) -> io::Result<Vec<ConfigLayerEntry>> {
+    let codex_home_abs = AbsolutePathBuf::from_absolute_path(codex_home)?;
+    let codex_home_normalized =
+        normalize_path(codex_home_abs.as_path()).unwrap_or_else(|_| codex_home_abs.to_path_buf());
     let mut dirs = cwd
         .as_path()
         .ancestors()
@@ -702,6 +708,11 @@ async fn load_project_layers(
         let layer_dir = AbsolutePathBuf::from_absolute_path(dir)?;
         let decision = trust_context.decision_for_dir(&layer_dir);
         let dot_codex_abs = AbsolutePathBuf::from_absolute_path(&dot_codex)?;
+        let dot_codex_normalized =
+            normalize_path(dot_codex_abs.as_path()).unwrap_or_else(|_| dot_codex_abs.to_path_buf());
+        if dot_codex_abs == codex_home_abs || dot_codex_normalized == codex_home_normalized {
+            continue;
+        }
         let config_file = dot_codex_abs.join(CONFIG_TOML_FILE)?;
         match tokio::fs::read_to_string(&config_file).await {
             Ok(contents) => {
diff --git a/codex-rs/core/src/config_loader/tests.rs b/codex-rs/core/src/config_loader/tests.rs
index 38d104fc19..355057f184 100644
--- a/codex-rs/core/src/config_loader/tests.rs
+++ b/codex-rs/core/src/config_loader/tests.rs
@@ -755,6 +755,101 @@ async fn project_layer_is_added_when_dot_codex_exists_without_config_toml() -> s
     Ok(())
 }
 
+#[tokio::test]
+async fn codex_home_is_not_loaded_as_project_layer_from_home_dir() -> std::io::Result<()> {
+    let tmp = tempdir()?;
+    let home_dir = tmp.path().join("home");
+    let codex_home = home_dir.join(".codex");
+    tokio::fs::create_dir_all(&codex_home).await?;
+    tokio::fs::write(codex_home.join(CONFIG_TOML_FILE), "foo = \"user\"\n").await?;
+
+    let cwd = AbsolutePathBuf::from_absolute_path(&home_dir)?;
+    let layers = load_config_layers_state(
+        &codex_home,
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+    )
+    .await?;
+
+    let project_layers: Vec<_> = layers
+        .get_layers(
+            super::ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            true,
+        )
+        .into_iter()
+        .filter(|layer| matches!(layer.name, super::ConfigLayerSource::Project { .. }))
+        .collect();
+    let expected: Vec<&ConfigLayerEntry> = Vec::new();
+    assert_eq!(expected, project_layers);
+    assert_eq!(
+        layers.effective_config().get("foo"),
+        Some(&TomlValue::String("user".to_string()))
+    );
+
+    Ok(())
+}
+
+#[tokio::test]
+async fn codex_home_within_project_tree_is_not_double_loaded() -> std::io::Result<()> {
+    let tmp = tempdir()?;
+    let project_root = tmp.path().join("project");
+    let nested = project_root.join("child");
+    let project_dot_codex = project_root.join(".codex");
+    let nested_dot_codex = nested.join(".codex");
+
+    tokio::fs::create_dir_all(&nested_dot_codex).await?;
+    tokio::fs::create_dir_all(project_root.join(".git")).await?;
+    tokio::fs::write(nested_dot_codex.join(CONFIG_TOML_FILE), "foo = \"child\"\n").await?;
+
+    tokio::fs::create_dir_all(&project_dot_codex).await?;
+    make_config_for_test(&project_dot_codex, &project_root, TrustLevel::Trusted, None).await?;
+    let user_config_path = project_dot_codex.join(CONFIG_TOML_FILE);
+    let user_config_contents = tokio::fs::read_to_string(&user_config_path).await?;
+    tokio::fs::write(
+        &user_config_path,
+        format!("foo = \"user\"\n{user_config_contents}"),
+    )
+    .await?;
+
+    let cwd = AbsolutePathBuf::from_absolute_path(&nested)?;
+    let layers = load_config_layers_state(
+        &project_dot_codex,
+        Some(cwd),
+        &[] as &[(String, TomlValue)],
+        LoaderOverrides::default(),
+    )
+    .await?;
+
+    let project_layers: Vec<_> = layers
+        .get_layers(
+            super::ConfigLayerStackOrdering::HighestPrecedenceFirst,
+            true,
+        )
+        .into_iter()
+        .filter(|layer| matches!(layer.name, super::ConfigLayerSource::Project { .. }))
+        .collect();
+
+    let child_config: TomlValue = toml::from_str("foo = \"child\"\n").expect("parse child config");
+    assert_eq!(
+        vec![&ConfigLayerEntry {
+            name: super::ConfigLayerSource::Project {
+                dot_codex_folder: AbsolutePathBuf::from_absolute_path(&nested_dot_codex)?,
+            },
+            config: child_config.clone(),
+            version: version_for_toml(&child_config),
+            disabled_reason: None,
+        }],
+        project_layers
+    );
+    assert_eq!(
+        layers.effective_config().get("foo"),
+        Some(&TomlValue::String("child".to_string()))
+    );
+
+    Ok(())
+}
+
 #[tokio::test]
 async fn project_layers_disabled_when_untrusted_or_unknown() -> std::io::Result<()> {
     let tmp = tempdir()?;