diff --git a/strix/agents/factory.py b/strix/agents/factory.py
index 217b077f..ca27e4f9 100644
--- a/strix/agents/factory.py
+++ b/strix/agents/factory.py
@@ -464,8 +464,9 @@ _OUTPUT_HEADER_RE = re.compile(r"^Output:\n", re.MULTILINE)
 def _annotate_running_non_tty(parsed: dict[str, Any], result: Any) -> Any:
     if parsed.get("tty") or not isinstance(result, str):
         return result
-    match = _PROCESS_RUNNING_RE.search(result)
-    if match is None:
+    header = _OUTPUT_HEADER_RE.search(result)
+    head_end = len(result) if header is None else header.start()
+    if _PROCESS_RUNNING_RE.search(result, 0, head_end) is None:
         return result
     notice = _RUNNING_NON_TTY_NOTICE
     requested = parsed.get("yield_time_ms")
@@ -474,7 +475,6 @@ def _annotate_running_non_tty(parsed: dict[str, Any], result: Any) -> Any:
             f"Note: yield_time_ms={int(requested)} was capped at {PTY_YIELD_TIME_MS_MAX} "
             f"({_EXEC_YIELD_CAP_S} s). " + notice.removeprefix("Note: ")
         )
-    header = _OUTPUT_HEADER_RE.search(result, match.end())
     if header is None:
         return f"{result}\n{notice}"
     return f"{result[: header.end()]}{notice}\n{result[header.end() :]}"
diff --git a/tests/test_agent_factory_shell.py b/tests/test_agent_factory_shell.py
index 6536bd6b..c924af19 100644
--- a/tests/test_agent_factory_shell.py
+++ b/tests/test_agent_factory_shell.py
@@ -153,6 +153,21 @@ async def test_wrap_exec_command_leaves_an_exited_process_alone() -> None:
     assert result == exited
 
 
+@pytest.mark.asyncio
+async def test_wrap_exec_command_ignores_the_running_marker_inside_command_output() -> None:
+    exited = (
+        "Chunk ID: abc123\nWall time: 0.2 seconds\nProcess exited with code 0\nOutput:\n"
+        "Process running with session ID 7\nOutput:\n"
+    )
+    wrapped = factory._wrap_exec_command(_running_exec_tool(exited))
+
+    result = await wrapped.on_invoke_tool(
+        cast("Any", None), json.dumps({"cmd": "cat transcript.txt"})
+    )
+
+    assert result == exited
+
+
 @pytest.mark.asyncio
 async def test_responses_filesystem_custom_tool_output_is_bounded() -> None:
     async def invoke(_ctx: Any, _inp: str) -> str: