diff --git a/tests/test_windows_subprocess_no_window_flags.py b/tests/test_windows_subprocess_no_window_flags.py
index 7768f5fec08..3777182167e 100644
--- a/tests/test_windows_subprocess_no_window_flags.py
+++ b/tests/test_windows_subprocess_no_window_flags.py
@@ -300,6 +300,44 @@ def test_local_stt_audio_prep_hides_ffmpeg_window(monkeypatch, tmp_path):
     assert captured[0][0][0] == "ffmpeg"
     assert captured[0][1]["creationflags"] == _CREATE_NO_WINDOW
 
+def test_checkpoint_manager_git_hides_windows(monkeypatch):
+    from tools import checkpoint_manager
+
+    captured = []
+
+    def fake_run(cmd, **kwargs):
+        captured.append((cmd, kwargs))
+        return _Completed(stdout="clean\n")
+
+    monkeypatch.setattr(checkpoint_manager, "IS_WINDOWS", True)
+    monkeypatch.setattr(checkpoint_manager, "windows_hide_flags", lambda: _CREATE_NO_WINDOW)
+    monkeypatch.setattr(checkpoint_manager.subprocess, "run", fake_run)
+
+    ok, _, _ = checkpoint_manager._run_git(["status", "--short"], Path("C:/store"), ".")
+    assert ok
+    assert captured[0][0][0] == "git"
+    assert captured[0][1]["creationflags"] == _CREATE_NO_WINDOW
+
+
+def test_skills_hub_gh_token_hides_windows(monkeypatch):
+    from tools import skills_hub
+
+    captured = []
+
+    def fake_run(cmd, **kwargs):
+        captured.append((cmd, kwargs))
+        return _Completed(stdout="gho_from_cli\n")
+
+    monkeypatch.setattr(skills_hub, "IS_WINDOWS", True)
+    monkeypatch.setattr(skills_hub, "windows_hide_flags", lambda: _CREATE_NO_WINDOW)
+    monkeypatch.setattr(skills_hub.subprocess, "run", fake_run)
+
+    auth = skills_hub.GitHubAuth.__new__(skills_hub.GitHubAuth)
+    assert auth._try_gh_cli() == "gho_from_cli"
+    assert captured[0][0] == ["gh", "auth", "token"]
+    assert captured[0][1]["creationflags"] == _CREATE_NO_WINDOW
+
+
 def test_tui_slash_worker_hides_python_window(monkeypatch):
     from tui_gateway import server
 
diff --git a/tools/checkpoint_manager.py b/tools/checkpoint_manager.py
index 720973b67e0..589c993ba6b 100644
--- a/tools/checkpoint_manager.py
+++ b/tools/checkpoint_manager.py
@@ -58,6 +58,7 @@ import subprocess
 import time
 from pathlib import Path
 from hermes_constants import get_hermes_home
+from hermes_cli._subprocess_compat import IS_WINDOWS, windows_hide_flags
 from typing import Dict, List, Optional, Set, Tuple
 
 from utils import env_int
@@ -321,6 +322,10 @@ def _run_git(
     env = _git_env(store, str(normalized_working_dir), index_file=index_file)
     cmd = ["git"] + list(args)
     allowed_returncodes = allowed_returncodes or set()
+    # Checkpoints run inside the console-less desktop/gateway backend; a bare
+    # git spawn there pops a fresh conhost window per call (status, add,
+    # commit, …) on Windows. No-op on POSIX.
+    _popen_kwargs = {"creationflags": windows_hide_flags()} if IS_WINDOWS else {}
     try:
         result = subprocess.run(
             cmd,
@@ -330,6 +335,7 @@ def _run_git(
             env=env,
             cwd=str(normalized_working_dir),
             stdin=subprocess.DEVNULL,
+            **_popen_kwargs,
         )
         ok = result.returncode == 0
         stdout = result.stdout.strip()
@@ -450,6 +456,7 @@ def _init_store(store: Path, working_dir: str) -> Optional[str]:
             capture_output=True, text=True,
             env=init_env, timeout=_GIT_TIMEOUT,
             stdin=subprocess.DEVNULL,
+            **({"creationflags": windows_hide_flags()} if IS_WINDOWS else {}),
         )
         if result.returncode != 0:
             return f"Shadow store init failed: {result.stderr.strip()}"
diff --git a/tools/skills_hub.py b/tools/skills_hub.py
index 76969fb8d8c..676b6c81f76 100644
--- a/tools/skills_hub.py
+++ b/tools/skills_hub.py
@@ -26,6 +26,7 @@ from dataclasses import dataclass, field
 from datetime import datetime, timezone
 from pathlib import Path, PurePosixPath
 from hermes_constants import get_hermes_home
+from hermes_cli._subprocess_compat import IS_WINDOWS, windows_hide_flags
 from agent.skill_utils import is_excluded_skill_path
 from typing import Any, Dict, List, Optional, Tuple, Union
 from urllib.parse import urljoin, urlparse, urlunparse
@@ -302,6 +303,7 @@ class GitHubAuth:
                 ["gh", "auth", "token"],
                 capture_output=True, text=True, timeout=5,
                 stdin=subprocess.DEVNULL,
+                **({"creationflags": windows_hide_flags()} if IS_WINDOWS else {}),
             )
             if result.returncode == 0 and result.stdout.strip():
                 return result.stdout.strip()