diff --git a/dify-agent/src/dify_agent/server/binding_files.py b/dify-agent/src/dify_agent/server/binding_files.py
index 8fee4be39c1..2ee12828ae9 100644
--- a/dify-agent/src/dify_agent/server/binding_files.py
+++ b/dify-agent/src/dify_agent/server/binding_files.py
@@ -50,6 +50,10 @@ import os
 import stat
 import sys
 
+# The shell transport may expose stdout only. Keep Python errors in the same
+# stream so the server can classify unavailable paths instead of returning 502.
+sys.stderr = sys.stdout
+
 path = sys.argv[1]
 response_path = sys.argv[2]
 limit = int(sys.argv[3])
@@ -89,6 +93,8 @@ import os
 import stat
 import sys
 
+sys.stderr = sys.stdout
+
 path = sys.argv[1]
 response_path = sys.argv[2]
 max_bytes = int(sys.argv[3])
diff --git a/dify-agent/tests/local/dify_agent/server/test_binding_files.py b/dify-agent/tests/local/dify_agent/server/test_binding_files.py
index 1df092289d2..53eb9f2be90 100644
--- a/dify-agent/tests/local/dify_agent/server/test_binding_files.py
+++ b/dify-agent/tests/local/dify_agent/server/test_binding_files.py
@@ -117,6 +117,8 @@ class _ProviderErrorCommands(_Commands):
 
 @dataclass(slots=True)
 class _LocalCommands(_Commands):
+    capture_stderr: bool = True
+
     async def run(
         self,
         script: str,
@@ -133,7 +135,7 @@ class _LocalCommands(_Commands):
             cwd=cwd,
             env={**os.environ, **(env or {})},
             stdout=asyncio.subprocess.PIPE,
-            stderr=asyncio.subprocess.STDOUT,
+            stderr=asyncio.subprocess.STDOUT if self.capture_stderr else asyncio.subprocess.DEVNULL,
         )
         output, _ = await asyncio.wait_for(process.communicate(), timeout=timeout)
         text = output.decode(errors="replace")
@@ -195,12 +197,16 @@ def _service(
     return service, backend
 
 
-def _local_service(tmp_path: Path) -> tuple[BindingFileService, _Backend, _LocalCommands, Path, Path]:
+def _local_service(
+    tmp_path: Path,
+    *,
+    capture_stderr: bool = True,
+) -> tuple[BindingFileService, _Backend, _LocalCommands, Path, Path]:
     workspace = tmp_path / "workspace"
     home = tmp_path / "home"
     workspace.mkdir()
     home.mkdir()
-    commands = _LocalCommands(outputs=[])
+    commands = _LocalCommands(outputs=[], capture_stderr=capture_stderr)
     backend = _Backend(
         lease=cast(
             RuntimeLease,
@@ -412,6 +418,21 @@ async def test_browse_preserves_binding_file_error_and_releases_lease(operation:
     assert backend.releases == 1
 
 
+@pytest.mark.parametrize("operation", ["list", "read"])
+@pytest.mark.anyio
+async def test_missing_path_is_classified_when_transport_only_captures_stdout(tmp_path: Path, operation: str) -> None:
+    service, backend, commands, _, _ = _local_service(tmp_path, capture_stderr=False)
+    with pytest.raises(BindingFileError) as error:
+        if operation == "list":
+            await service.list_files(BindingFileListRequest(backend_binding_ref="binding-ref", path="missing"))
+        else:
+            await service.read_file(BindingFileReadRequest(backend_binding_ref="binding-ref", path="missing"))
+    assert error.value.code == "invalid_binding_path"
+    assert error.value.status_code == 400
+    assert backend.releases == 1
+    assert commands.deletes == ["local-job-1"]
+
+
 @pytest.mark.parametrize("operation", ["list", "read"])
 @pytest.mark.anyio
 async def test_browse_maps_malformed_backend_response_to_unavailable_and_releases_lease(operation: str) -> None: