diff --git a/hermes_cli/mcp_startup.py b/hermes_cli/mcp_startup.py
index e4d34c75e06..ad9996e65b9 100644
--- a/hermes_cli/mcp_startup.py
+++ b/hermes_cli/mcp_startup.py
@@ -98,3 +98,33 @@ def wait_for_mcp_discovery(timeout: "float | None" = None) -> None:
     if thread is None or not thread.is_alive():
         return
     thread.join(timeout=_resolve_discovery_timeout(timeout))
+
+
+def mcp_discovery_in_flight() -> bool:
+    """Return True if THIS module's background discovery thread is still running.
+
+    Mirrors ``tui_gateway.entry.mcp_discovery_in_flight`` for the surfaces that
+    start discovery through ``start_background_mcp_discovery`` here (the desktop
+    app + dashboard WebSocket sidecar via ``tui_gateway/ws.py``, and
+    ``hermes dashboard``).  Those processes populate THIS module's
+    ``_mcp_discovery_thread``, not ``tui_gateway.entry``'s, so the late-refresh
+    scheduler must consult both to decide whether a slow server's tools are
+    still pending (see #51587).
+    """
+    thread = _mcp_discovery_thread
+    return thread is not None and thread.is_alive()
+
+
+def join_mcp_discovery(timeout: "float | None" = None) -> bool:
+    """Block until THIS module's background discovery finishes, up to ``timeout``.
+
+    Returns True if discovery has completed (thread absent or no longer alive),
+    False if it is still running after the timeout.  Unlike
+    ``wait_for_mcp_discovery`` this accepts an unbounded/long wait and reports
+    the outcome, for the off-critical-path late-refresh waiter.
+    """
+    thread = _mcp_discovery_thread
+    if thread is None:
+        return True
+    thread.join(timeout=timeout)
+    return not thread.is_alive()
diff --git a/tests/tui_gateway/test_mcp_late_refresh_thread_owner.py b/tests/tui_gateway/test_mcp_late_refresh_thread_owner.py
new file mode 100644
index 00000000000..b793b9fd048
--- /dev/null
+++ b/tests/tui_gateway/test_mcp_late_refresh_thread_owner.py
@@ -0,0 +1,119 @@
+"""Regression test for issue #51587.
+
+MCP tools connected/enabled but never surfaced into the agent's session
+toolset on the desktop app + dashboard WebUI.
+
+Root cause: there are two independent background MCP discovery thread owners
+by surface:
+
+  * ``tui_gateway.entry`` — the stdio ``hermes --tui`` path.
+  * ``hermes_cli.mcp_startup`` — the desktop app + dashboard WebSocket sidecar
+    (``tui_gateway/ws.py``) and ``hermes dashboard``.
+
+The late-refresh scheduler (``tui_gateway.server._schedule_mcp_late_refresh``)
+gates on ``tui_gateway.entry.mcp_discovery_in_flight()``. Before the fix that
+function read ONLY ``tui_gateway.entry._mcp_discovery_thread``. On the
+desktop/dashboard surfaces that thread is ``None`` (the thread lives on
+``hermes_cli.mcp_startup``), so the scheduler bailed immediately and a slow MCP
+server's tools never surfaced for the whole session — even after a container
+restart. The fix makes ``mcp_discovery_in_flight`` / ``join_mcp_discovery``
+consult BOTH thread owners.
+"""
+
+import threading
+
+import pytest
+
+import hermes_cli.mcp_startup as startup
+import tui_gateway.entry as entry
+
+
+@pytest.fixture
+def clean_discovery_globals():
+    """Snapshot and restore both modules' discovery-thread globals."""
+    saved_entry = entry._mcp_discovery_thread
+    saved_startup = startup._mcp_discovery_thread
+    entry._mcp_discovery_thread = None
+    startup._mcp_discovery_thread = None
+    try:
+        yield
+    finally:
+        entry._mcp_discovery_thread = saved_entry
+        startup._mcp_discovery_thread = saved_startup
+
+
+def _alive_thread(stop: threading.Event) -> threading.Thread:
+    t = threading.Thread(target=lambda: stop.wait(5.0), daemon=True)
+    t.start()
+    return t
+
+
+def test_entry_in_flight_sees_startup_thread(clean_discovery_globals):
+    """Desktop/dashboard surface: discovery thread lives on hermes_cli.mcp_startup.
+
+    The entry-level in-flight check must report True so the late-refresh
+    scheduler does not bail (the #51587 bug).
+    """
+    stop = threading.Event()
+    startup._mcp_discovery_thread = _alive_thread(stop)
+    try:
+        # Entry's own thread is None, but the startup thread is alive.
+        assert entry._mcp_discovery_thread is None
+        assert entry.mcp_discovery_in_flight() is True
+    finally:
+        stop.set()
+        startup._mcp_discovery_thread.join(timeout=2.0)
+
+    # After the thread exits, neither owner is in flight.
+    assert entry.mcp_discovery_in_flight() is False
+
+
+def test_entry_join_waits_on_startup_thread(clean_discovery_globals):
+    """join_mcp_discovery must report not-done while the startup thread runs."""
+    stop = threading.Event()
+    t = _alive_thread(stop)
+    startup._mcp_discovery_thread = t
+
+    assert entry.join_mcp_discovery(timeout=0.1) is False
+
+    stop.set()
+    t.join(timeout=2.0)
+    assert entry.join_mcp_discovery(timeout=2.0) is True
+
+
+def test_entry_in_flight_still_sees_own_thread(clean_discovery_globals):
+    """stdio TUI surface: discovery thread lives on tui_gateway.entry (unchanged)."""
+    stop = threading.Event()
+    entry._mcp_discovery_thread = _alive_thread(stop)
+    try:
+        assert startup._mcp_discovery_thread is None
+        assert entry.mcp_discovery_in_flight() is True
+    finally:
+        stop.set()
+        entry._mcp_discovery_thread.join(timeout=2.0)
+
+    assert entry.mcp_discovery_in_flight() is False
+
+
+def test_no_mcp_threads_not_in_flight(clean_discovery_globals):
+    """No discovery anywhere → not in flight, join reports done immediately."""
+    assert entry.mcp_discovery_in_flight() is False
+    assert entry.join_mcp_discovery(timeout=0.1) is True
+
+
+def test_startup_module_exposes_in_flight_helpers(clean_discovery_globals):
+    """hermes_cli.mcp_startup gains the in-flight/join helpers entry delegates to."""
+    assert startup.mcp_discovery_in_flight() is False
+    assert startup.join_mcp_discovery(timeout=0.1) is True
+
+    stop = threading.Event()
+    t = _alive_thread(stop)
+    startup._mcp_discovery_thread = t
+    try:
+        assert startup.mcp_discovery_in_flight() is True
+        assert startup.join_mcp_discovery(timeout=0.1) is False
+    finally:
+        stop.set()
+        t.join(timeout=2.0)
+    assert startup.mcp_discovery_in_flight() is False
+    assert startup.join_mcp_discovery(timeout=2.0) is True
diff --git a/tui_gateway/entry.py b/tui_gateway/entry.py
index 0a39e69766e..c738330f6dc 100644
--- a/tui_gateway/entry.py
+++ b/tui_gateway/entry.py
@@ -233,30 +233,61 @@ def wait_for_mcp_discovery(timeout: "float | None" = None) -> None:
 
 
 def mcp_discovery_in_flight() -> bool:
-    """Return True if the background MCP discovery thread is still running.
+    """Return True if ANY background MCP discovery thread is still running.
 
     Used by the agent-build path to decide whether to schedule a late tool
     snapshot refresh: if discovery didn't land within the bounded
     ``wait_for_mcp_discovery`` join, the agent was built without those tools
     and the banner/tool count will be stale until they arrive.
+
+    There are two independent discovery-thread owners by surface: the stdio
+    ``hermes --tui`` path spawns ITS thread here (``_mcp_discovery_thread``),
+    while the desktop app + dashboard WebSocket sidecar (``tui_gateway/ws.py``)
+    and ``hermes dashboard`` spawn theirs via
+    ``hermes_cli.mcp_startup.start_background_mcp_discovery``. The late-refresh
+    scheduler imports this function regardless of surface, so it MUST consult
+    both — checking only the entry thread left the desktop/dashboard surfaces
+    with no late refresh, so a slow MCP server's tools never surfaced for the
+    whole session (#51587).
     """
     thread = _mcp_discovery_thread
-    return thread is not None and thread.is_alive()
+    if thread is not None and thread.is_alive():
+        return True
+    try:
+        from hermes_cli.mcp_startup import (
+            mcp_discovery_in_flight as _startup_in_flight,
+        )
+
+        return _startup_in_flight()
+    except Exception:
+        return False
 
 
 def join_mcp_discovery(timeout: float | None = None) -> bool:
     """Block until background MCP discovery finishes, up to ``timeout`` seconds.
 
-    Returns True if discovery has completed (thread absent or no longer alive),
-    False if it is still running after the timeout. Unlike
+    Returns True if discovery has completed (both thread owners absent or no
+    longer alive), False if either is still running after the timeout. Unlike
     ``wait_for_mcp_discovery`` this accepts an unbounded/long wait and reports
     the outcome, for the off-critical-path late-refresh waiter.
+
+    Joins both discovery-thread owners (see ``mcp_discovery_in_flight``): the
+    entry thread first, then the ``hermes_cli.mcp_startup`` thread used by the
+    desktop/dashboard surfaces. ``timeout`` bounds EACH join, mirroring the
+    pre-#51587 single-owner behavior for the entry thread.
     """
+    entry_done = True
     thread = _mcp_discovery_thread
-    if thread is None:
-        return True
-    thread.join(timeout=timeout)
-    return not thread.is_alive()
+    if thread is not None:
+        thread.join(timeout=timeout)
+        entry_done = not thread.is_alive()
+    try:
+        from hermes_cli.mcp_startup import join_mcp_discovery as _startup_join
+
+        startup_done = _startup_join(timeout=timeout)
+    except Exception:
+        startup_done = True
+    return entry_done and startup_done
 
 
 def main():