diff --git a/litellm/proxy/_experimental/mcp_server/byok_oauth_endpoints.py b/litellm/proxy/_experimental/mcp_server/byok_oauth_endpoints.py
index 0721c2c5ace..0ab76588b1f 100644
--- a/litellm/proxy/_experimental/mcp_server/byok_oauth_endpoints.py
+++ b/litellm/proxy/_experimental/mcp_server/byok_oauth_endpoints.py
@@ -34,6 +34,7 @@ from litellm.proxy._experimental.mcp_server.oauth_utils import (
     well_known_root_suffix,
 )
 from litellm.proxy._types import UserAPIKeyAuth
+from litellm.proxy.middleware.per_request_root_path_middleware import get_server_root_paths
 
 # ---------------------------------------------------------------------------
 # In-memory store for pending authorization codes.
@@ -620,6 +621,16 @@ async def byok_authorization_server_metadata(request: Request) -> JSONResponse:
     return _byok_authorization_server_response(base_url, f"{base_url}/v1/mcp/oauth")
 
 
+@router.get("/.well-known/oauth-authorization-server/{root_path:path}/v1/mcp/oauth", include_in_schema=False)
+async def byok_prefixed_authorization_server_metadata(request: Request, root_path: str) -> JSONResponse:
+    prefix: Final = f"/{root_path}"
+    if prefix not in get_server_root_paths():
+        raise HTTPException(status_code=404, detail="Unknown proxy root path")
+    parsed: Final = urlparse(get_request_base_url(request))
+    base_url: Final = f"{parsed.scheme}://{parsed.netloc}{prefix}"
+    return _byok_authorization_server_response(base_url, f"{base_url}/v1/mcp/oauth")
+
+
 @router.get(BYOK_RESOURCE_METADATA_PATH, include_in_schema=False)
 async def byok_protected_resource_metadata(request: Request) -> JSONResponse:
     base_url: Final = get_request_base_url(request)
diff --git a/litellm/proxy/_experimental/mcp_server/oauth_utils.py b/litellm/proxy/_experimental/mcp_server/oauth_utils.py
index fe35c87e07c..39865a35ec6 100644
--- a/litellm/proxy/_experimental/mcp_server/oauth_utils.py
+++ b/litellm/proxy/_experimental/mcp_server/oauth_utils.py
@@ -16,6 +16,7 @@ from litellm.proxy._experimental.mcp_server.auth.token_endpoint_auth import (
     normalize_token_endpoint_auth_method,
 )
 from litellm.proxy.auth.ip_address_utils import IPAddressUtils
+from litellm.proxy.middleware.per_request_root_path_middleware import get_request_root_path
 
 if TYPE_CHECKING:
     from litellm.types.mcp_server.mcp_server_manager import MCPServer
@@ -130,7 +131,7 @@ BYOK_RESOURCE_METADATA_PATH: Final = "/v1/mcp/oauth/protected-resource"
 
 
 def get_byok_www_authenticate() -> str:
-    base_url: Final = _resolve_proxy_base_url_env() or well_known_root_suffix()
+    base_url: Final = _resolve_proxy_base_url_env() or get_request_root_path().rstrip("/")
     return f'Bearer resource_metadata="{base_url}{BYOK_RESOURCE_METADATA_PATH}"'
 
 
diff --git a/tests/test_litellm/proxy/_experimental/mcp_server/test_byok_oauth_endpoints.py b/tests/test_litellm/proxy/_experimental/mcp_server/test_byok_oauth_endpoints.py
index 2b4fa572b76..55accfb169d 100644
--- a/tests/test_litellm/proxy/_experimental/mcp_server/test_byok_oauth_endpoints.py
+++ b/tests/test_litellm/proxy/_experimental/mcp_server/test_byok_oauth_endpoints.py
@@ -142,6 +142,43 @@ def test_byok_challenge_preserves_external_base(monkeypatch, base_url, root_path
     assert get_byok_www_authenticate() == f'Bearer resource_metadata="{expected}"'
 
 
+def test_byok_discovery_preserves_per_request_prefixes(monkeypatch):
+    from fastapi import FastAPI
+
+    from litellm.proxy._experimental.mcp_server.server import _check_byok_credential
+    from litellm.proxy.middleware.per_request_root_path_middleware import PerRequestRootPathMiddleware
+    from litellm.types.mcp_server.mcp_server_manager import MCPServer
+
+    monkeypatch.delenv("PROXY_BASE_URL", raising=False)
+    monkeypatch.delenv("SERVER_ROOT_PATH", raising=False)
+    monkeypatch.setenv("SERVER_ROOT_PATHS", "/tenant-a,/tenant-b")
+    app = FastAPI()
+    app.include_router(router)
+    app.add_middleware(PerRequestRootPathMiddleware, root_paths=("/tenant-a", "/tenant-b"))
+    server = MCPServer(server_id="byok-prefix", name="byok-prefix", transport=MCPTransport.http, is_byok=True)
+
+    @app.get("/challenge")
+    async def challenge():
+        await _check_byok_credential(server, None)
+
+    with TestClient(app) as client:
+        for prefix in ("/tenant-a", "/tenant-b", ""):
+            challenge_response = client.get(f"{prefix}/challenge")
+            assert challenge_response.status_code == 401
+            metadata_path = f"{prefix}/v1/mcp/oauth/protected-resource"
+            assert challenge_response.headers["www-authenticate"] == f'Bearer resource_metadata="{metadata_path}"'
+            prm = client.get(metadata_path)
+            assert prm.status_code == 200
+            issuer = f"http://testserver{prefix}/v1/mcp/oauth"
+            assert prm.json()["authorization_servers"] == [issuer]
+            asm = client.get(f"/.well-known/oauth-authorization-server{prefix}/v1/mcp/oauth")
+            assert asm.status_code == 200
+            assert asm.json()["issuer"] == issuer
+            assert asm.json()["authorization_endpoint"] == f"{issuer}/authorize"
+            assert asm.json()["token_endpoint"] == f"{issuer}/token"
+        assert client.get("/.well-known/oauth-authorization-server/unknown/v1/mcp/oauth").status_code == 404
+
+
 def test_oauth_authorization_server_metadata(client):
     resp = client.get("/.well-known/oauth-authorization-server")
     assert resp.status_code == 200