diff --git a/hermes_cli/mcp_config.py b/hermes_cli/mcp_config.py
index 17b6c0329e5..575d5f9b5ee 100644
--- a/hermes_cli/mcp_config.py
+++ b/hermes_cli/mcp_config.py
@@ -212,7 +212,7 @@ def _probe_single_server(
         _ensure_mcp_loop,
         _run_on_mcp_loop,
         _connect_server,
-        _stop_mcp_loop,
+        _stop_mcp_loop_if_idle,
     )
 
     config = _resolve_mcp_server_config(config)
@@ -240,7 +240,7 @@ def _probe_single_server(
     except BaseException as exc:
         raise _unwrap_exception_group(exc) from None
     finally:
-        _stop_mcp_loop()
+        _stop_mcp_loop_if_idle()
 
     return tools_found
 
diff --git a/tests/tools/test_mcp_probe.py b/tests/tools/test_mcp_probe.py
index 89d4d1478d1..92656a441b3 100644
--- a/tests/tools/test_mcp_probe.py
+++ b/tests/tools/test_mcp_probe.py
@@ -162,14 +162,14 @@ class TestProbeMcpServerTools:
         assert result["github"][0] == ("my_tool", "")
 
     def test_cleanup_called_even_on_failure(self):
-        """_stop_mcp_loop is called even when probe fails."""
+        """Probe cleanup is attempted even when probe fails."""
         config = {"github": {"command": "npx", "connect_timeout": 5}}
 
         with patch("tools.mcp_tool._MCP_AVAILABLE", True), \
              patch("tools.mcp_tool._load_mcp_config", return_value=config), \
              patch("tools.mcp_tool._ensure_mcp_loop"), \
              patch("tools.mcp_tool._run_on_mcp_loop", side_effect=RuntimeError("boom")), \
-             patch("tools.mcp_tool._stop_mcp_loop") as mock_stop:
+             patch("tools.mcp_tool._stop_mcp_loop_if_idle") as mock_stop:
 
             from tools.mcp_tool import probe_mcp_server_tools
             result = probe_mcp_server_tools()
diff --git a/tests/tools/test_mcp_stability.py b/tests/tools/test_mcp_stability.py
index 3897a65a866..feb0d7a5aff 100644
--- a/tests/tools/test_mcp_stability.py
+++ b/tests/tools/test_mcp_stability.py
@@ -57,6 +57,32 @@ class TestMCPLoopExceptionHandler:
         finally:
             mcp_mod._stop_mcp_loop()
 
+    def test_probe_cleanup_does_not_stop_loop_with_registered_servers(self):
+        """Probe cleanup must not kill the shared loop used by live MCP tools."""
+        import tools.mcp_tool as mcp_mod
+
+        with mcp_mod._lock:
+            mcp_mod._servers.clear()
+            mcp_mod._server_connecting.clear()
+        try:
+            mcp_mod._ensure_mcp_loop()
+            with mcp_mod._lock:
+                loop = mcp_mod._mcp_loop
+                mcp_mod._servers["live"] = MagicMock(session=object())
+
+            assert mcp_mod._stop_mcp_loop_if_idle() is False
+
+            with mcp_mod._lock:
+                assert mcp_mod._mcp_loop is loop
+                assert mcp_mod._mcp_thread is not None
+            assert loop is not None
+            assert loop.is_running()
+        finally:
+            with mcp_mod._lock:
+                mcp_mod._servers.clear()
+                mcp_mod._server_connecting.clear()
+            mcp_mod._stop_mcp_loop()
+
 
 # ---------------------------------------------------------------------------
 # Fix 2: stdio PID tracking
diff --git a/tools/mcp_tool.py b/tools/mcp_tool.py
index 1317b14dc35..3b0224b59b4 100644
--- a/tools/mcp_tool.py
+++ b/tools/mcp_tool.py
@@ -3946,7 +3946,7 @@ def probe_mcp_server_tools() -> Dict[str, List[tuple]]:
     except Exception as exc:
         logger.debug("MCP probe failed: %s", exc)
     finally:
-        _stop_mcp_loop()
+        _stop_mcp_loop_if_idle()
 
     return result
 
@@ -4084,10 +4084,25 @@ def _kill_orphaned_mcp_children(include_active: bool = False) -> None:
         )
 
 
-def _stop_mcp_loop():
+def _stop_mcp_loop_if_idle() -> bool:
+    """Stop the MCP loop only when no registered server still owns it.
+
+    Probe paths create temporary MCPServerTask instances that are not placed in
+    ``_servers``.  They should clean up an otherwise-idle loop, but must not
+    tear down the process-global loop when live agent tools are registered on
+    it.  Otherwise a dashboard/CLI probe can make later MCP tool calls fail
+    with ``MCP event loop is not running``.
+    """
+    return _stop_mcp_loop(only_if_idle=True)
+
+
+def _stop_mcp_loop(*, only_if_idle: bool = False) -> bool:
     """Stop the background event loop and join its thread."""
     global _mcp_loop, _mcp_thread
     with _lock:
+        if only_if_idle and (_servers or _server_connecting):
+            logger.debug("Leaving MCP event loop running; active servers are registered or connecting")
+            return False
         loop = _mcp_loop
         thread = _mcp_thread
         _mcp_loop = None
@@ -4104,3 +4119,4 @@ def _stop_mcp_loop():
         # graceful shutdown are now orphaned — include active PIDs too
         # since the loop is gone and no session can still be in flight.
         _kill_orphaned_mcp_children(include_active=True)
+    return True