diff --git a/codex-rs/exec/src/event_processor_with_human_output.rs b/codex-rs/exec/src/event_processor_with_human_output.rs
index 00a9f957f..60667bb5d 100644
--- a/codex-rs/exec/src/event_processor_with_human_output.rs
+++ b/codex-rs/exec/src/event_processor_with_human_output.rs
@@ -239,6 +239,7 @@ impl EventProcessor for EventProcessorWithHumanOutput {
                 );
                 CodexStatus::Running
             }
+            ServerNotification::Warning(notification) => self.process_warning(notification.message),
             ServerNotification::Error(notification) => {
                 eprintln!(
                     "{} {}",
diff --git a/codex-rs/exec/src/event_processor_with_jsonl_output.rs b/codex-rs/exec/src/event_processor_with_jsonl_output.rs
index 89e41eacb..79bf88eaa 100644
--- a/codex-rs/exec/src/event_processor_with_jsonl_output.rs
+++ b/codex-rs/exec/src/event_processor_with_jsonl_output.rs
@@ -430,6 +430,11 @@ impl EventProcessorWithJsonOutput {
                 }));
                 CodexStatus::Running
             }
+            ServerNotification::Warning(notification) => {
+                let warning = self.collect_warning(notification.message);
+                events.extend(warning.events);
+                warning.status
+            }
             ServerNotification::Error(notification) => {
                 let message = match notification.error.additional_details {
                     Some(details) if !details.is_empty() => {
diff --git a/codex-rs/exec/src/event_processor_with_jsonl_output_tests.rs b/codex-rs/exec/src/event_processor_with_jsonl_output_tests.rs
index b8b0267fc..f8521071e 100644
--- a/codex-rs/exec/src/event_processor_with_jsonl_output_tests.rs
+++ b/codex-rs/exec/src/event_processor_with_jsonl_output_tests.rs
@@ -59,6 +59,33 @@ fn failed_turn_does_not_overwrite_output_last_message_file() {
     );
 }
 
+#[test]
+fn runtime_warning_emits_a_non_fatal_error_item() {
+    let mut processor = EventProcessorWithJsonOutput::new(/*last_message_path*/ None);
+
+    let collected = processor.collect_thread_events(ServerNotification::Warning(
+        codex_app_server_protocol::WarningNotification {
+            thread_id: Some("thread-1".to_string()),
+            message: "invalid global instructions".to_string(),
+        },
+    ));
+
+    assert_eq!(
+        collected,
+        CollectedThreadEvents {
+            events: vec![ThreadEvent::ItemCompleted(ItemCompletedEvent {
+                item: ExecThreadItem {
+                    id: "item_0".to_string(),
+                    details: ThreadItemDetails::Error(ErrorItem {
+                        message: "invalid global instructions".to_string(),
+                    }),
+                },
+            })],
+            status: CodexStatus::Running,
+        }
+    );
+}
+
 #[test]
 fn mcp_tool_call_result_preserves_meta_in_jsonl_event() {
     let mut processor = EventProcessorWithJsonOutput::new(/*last_message_path*/ None);
diff --git a/codex-rs/exec/src/lib.rs b/codex-rs/exec/src/lib.rs
index fbecfe562..5dce65d71 100644
--- a/codex-rs/exec/src/lib.rs
+++ b/codex-rs/exec/src/lib.rs
@@ -1256,6 +1256,11 @@ fn should_process_notification(
 ) -> bool {
     match notification {
         ServerNotification::ConfigWarning(_) | ServerNotification::DeprecationNotice(_) => true,
+        // TODO(anp) resolve duplicate startup warnings
+        ServerNotification::Warning(notification) => notification
+            .thread_id
+            .as_deref()
+            .is_none_or(|candidate| candidate == thread_id),
         ServerNotification::Error(notification) => {
             notification.thread_id == thread_id && notification.turn_id == turn_id
         }
diff --git a/codex-rs/exec/src/lib_tests.rs b/codex-rs/exec/src/lib_tests.rs
index 8b2f21498..de81f60d7 100644
--- a/codex-rs/exec/src/lib_tests.rs
+++ b/codex-rs/exec/src/lib_tests.rs
@@ -267,6 +267,35 @@ fn lagged_event_warning_message_is_explicit() {
     );
 }
 
+#[test]
+fn runtime_warnings_are_filtered_to_the_primary_thread() {
+    let primary_thread_id = "thread-1";
+    let turn_id = "turn-1";
+    let outcomes = [
+        codex_app_server_protocol::WarningNotification {
+            thread_id: None,
+            message: "global warning".to_string(),
+        },
+        codex_app_server_protocol::WarningNotification {
+            thread_id: Some(primary_thread_id.to_string()),
+            message: "primary warning".to_string(),
+        },
+        codex_app_server_protocol::WarningNotification {
+            thread_id: Some("thread-2".to_string()),
+            message: "other warning".to_string(),
+        },
+    ]
+    .map(|warning| {
+        should_process_notification(
+            &ServerNotification::Warning(warning),
+            primary_thread_id,
+            turn_id,
+        )
+    });
+
+    assert_eq!(outcomes, [true, true, false]);
+}
+
 #[tokio::test]
 async fn resume_lookup_model_providers_filters_only_last_lookup() {
     let codex_home = tempdir().expect("create temp codex home");
diff --git a/codex-rs/exec/tests/suite/agents_md.rs b/codex-rs/exec/tests/suite/agents_md.rs
index 2891721ae..d2a53d88e 100644
--- a/codex-rs/exec/tests/suite/agents_md.rs
+++ b/codex-rs/exec/tests/suite/agents_md.rs
@@ -2,6 +2,8 @@
 
 use core_test_support::responses;
 use core_test_support::test_codex_exec::test_codex_exec;
+use predicates::prelude::PredicateBooleanExt;
+use predicates::str::contains;
 
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
 async fn exec_includes_workspace_agents_md_in_request() -> anyhow::Result<()> {
@@ -72,3 +74,71 @@ async fn exec_prefers_workspace_agents_override_md() -> anyhow::Result<()> {
 
     Ok(())
 }
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn exec_surfaces_project_instruction_loading_warnings() -> anyhow::Result<()> {
+    let test = test_codex_exec();
+    let project_agents_path = test.cwd_path().join("AGENTS.md");
+    std::fs::write(&project_agents_path, b"project\xFFinstructions")?;
+
+    let server = responses::start_mock_server().await;
+    let body = responses::sse(vec![
+        responses::ev_response_created("resp1"),
+        responses::ev_assistant_message("m1", "fixture hello"),
+        responses::ev_completed("resp1"),
+    ]);
+    responses::mount_sse_once(&server, body).await;
+
+    test.cmd_with_server(&server)
+        .arg("--skip-git-repo-check")
+        .arg("tell me something")
+        .assert()
+        .success()
+        .stderr(contains("invalid UTF-8").and(contains(project_agents_path.display().to_string())));
+
+    Ok(())
+}
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn exec_json_surfaces_project_instruction_loading_warnings() -> anyhow::Result<()> {
+    let test = test_codex_exec();
+    let project_agents_path = test.cwd_path().join("AGENTS.md");
+    std::fs::write(&project_agents_path, b"project\xFFinstructions")?;
+
+    let server = responses::start_mock_server().await;
+    let body = responses::sse(vec![
+        responses::ev_response_created("resp1"),
+        responses::ev_assistant_message("m1", "fixture hello"),
+        responses::ev_completed("resp1"),
+    ]);
+    responses::mount_sse_once(&server, body).await;
+
+    let output = test
+        .cmd_with_server(&server)
+        .arg("--skip-git-repo-check")
+        .arg("--json")
+        .arg("tell me something")
+        .assert()
+        .success()
+        .get_output()
+        .stdout
+        .clone();
+    let events = String::from_utf8(output)?
+        .lines()
+        .map(serde_json::from_str::<serde_json::Value>)
+        .collect::<Result<Vec<_>, _>>()?;
+
+    assert!(
+        events.iter().any(|event| {
+            event["type"] == "item.completed"
+                && event["item"]["type"] == "error"
+                && event["item"]["message"].as_str().is_some_and(|message| {
+                    message.contains("invalid UTF-8")
+                        && message.contains(project_agents_path.display().to_string().as_str())
+                })
+        }),
+        "expected a JSONL warning event; observed: {events:?}"
+    );
+
+    Ok(())
+}