diff --git a/litellm/proxy/pass_through_endpoints/pass_through_endpoints.py b/litellm/proxy/pass_through_endpoints/pass_through_endpoints.py
index 970cd466337..515491f938f 100644
--- a/litellm/proxy/pass_through_endpoints/pass_through_endpoints.py
+++ b/litellm/proxy/pass_through_endpoints/pass_through_endpoints.py
@@ -674,8 +674,13 @@ class HttpPassThroughEndpointHelpers(BasePassthroughUtils):
         )
 
         litellm_keys_in_body: Final = MappingProxyType(
-            {k: _parsed_body.pop(k) for k in types_utils.all_litellm_params if k in _parsed_body}
+            {k: _parsed_body[k] for k in types_utils.all_litellm_params if k in _parsed_body}
         )
+        if request_dispatched_to_pass_through_endpoint(request):
+            _parsed_body.pop("litellm_logging_obj", None)
+        else:
+            for key in litellm_keys_in_body:
+                _parsed_body.pop(key)
         kept_out_of_litellm_params: Final = (
             _KEPT_OUT_OF_LITELLM_PARAMS
             if _key_or_team_allows_client_pricing_override(user_api_key_dict)
diff --git a/tests/unit/proxy/pass_through_endpoints/test_pass_through_endpoints.py b/tests/unit/proxy/pass_through_endpoints/test_pass_through_endpoints.py
index 4fe358c38a3..3e103a20f55 100644
--- a/tests/unit/proxy/pass_through_endpoints/test_pass_through_endpoints.py
+++ b/tests/unit/proxy/pass_through_endpoints/test_pass_through_endpoints.py
@@ -74,6 +74,7 @@ from litellm.types.guardrails import GuardrailEventHooks
 from litellm.types.utils import CallTypes
 from litellm.types.passthrough_endpoints.pass_through_endpoints import (
     LITELLM_PASS_THROUGH_DEPLOYMENT_MODEL_INFO_STATE_KEY,
+    LITELLM_PASS_THROUGH_ENDPOINT_MARKER,
     LITELLM_PASS_THROUGH_RAW_BODY_STATE_KEY,
     EndpointType,
     PassthroughStandardLoggingPayload,
@@ -6638,6 +6639,7 @@ async def _relay_through_pass_through(
     target: str,
     guardrails_config: dict[str, object] | None,
     custom_body: dict[str, object] | None = None,
+    custom_endpoint: bool = False,
 ) -> Mapping[str, object]:
     async def receive() -> Mapping[str, object]:
         return {"type": "http.request", "body": json.dumps(dict(client_body)).encode()}
@@ -6649,6 +6651,7 @@ async def _relay_through_pass_through(
             "path": "/my-claude-route",
             "query_string": b"",
             "headers": [(b"content-type", b"application/json")],
+            "endpoint": SimpleNamespace(**{LITELLM_PASS_THROUGH_ENDPOINT_MARKER: True}) if custom_endpoint else None,
         },
         receive,
     )
@@ -6676,6 +6679,17 @@ async def _relay_through_pass_through(
     return MappingProxyType(json.loads(relayed))
 
 
+@pytest.mark.parametrize("request_id", [1, "request-1", None])
+async def test_custom_pass_through_preserves_json_rpc_request_id(request_id: int | str | None) -> None:
+    body: Final = {"jsonrpc": "2.0", "id": request_id, "method": "skills/list", "params": {}, "canary": "kept"}
+
+    upstream_body: Final = await _relay_through_pass_through(
+        body, "http://upstream.test/mcp", guardrails_config=None, custom_endpoint=True
+    )
+
+    assert upstream_body == body
+
+
 _MESSAGES_BODY: Final = MappingProxyType(
     {"model": "claude-sonnet-4-5", "max_tokens": 16, "messages": [{"role": "user", "content": "hi"}]}
 )