diff --git a/hermes_cli/tools_config.py b/hermes_cli/tools_config.py
index 1bc1c643551..3f94bbc30b0 100644
--- a/hermes_cli/tools_config.py
+++ b/hermes_cli/tools_config.py
@@ -391,18 +391,29 @@ def _get_platform_tools(config: dict, platform: str) -> Set[str]:
         default_ts = PLATFORMS[platform]["default_toolset"]
         toolset_names = [default_ts]
 
-    # Resolve to individual tool names, then map back to which
-    # configurable toolsets are covered
-    all_tool_names = set()
-    for ts_name in toolset_names:
-        all_tool_names.update(resolve_toolset(ts_name))
+    configurable_keys = {ts_key for ts_key, _, _ in CONFIGURABLE_TOOLSETS}
 
-    # Map individual tool names back to configurable toolset keys
-    enabled_toolsets = set()
-    for ts_key, _, _ in CONFIGURABLE_TOOLSETS:
-        ts_tools = set(resolve_toolset(ts_key))
-        if ts_tools and ts_tools.issubset(all_tool_names):
-            enabled_toolsets.add(ts_key)
+    # If the saved list contains any configurable keys directly, the user
+    # has explicitly configured this platform — use direct membership.
+    # This avoids the subset-inference bug where composite toolsets like
+    # "hermes-cli" (which include all _HERMES_CORE_TOOLS) cause disabled
+    # toolsets to re-appear as enabled.
+    has_explicit_config = any(ts in configurable_keys for ts in toolset_names)
+
+    if has_explicit_config:
+        enabled_toolsets = {ts for ts in toolset_names if ts in configurable_keys}
+    else:
+        # No explicit config — fall back to resolving composite toolset names
+        # (e.g. "hermes-cli") to individual tool names and reverse-mapping.
+        all_tool_names = set()
+        for ts_name in toolset_names:
+            all_tool_names.update(resolve_toolset(ts_name))
+
+        enabled_toolsets = set()
+        for ts_key, _, _ in CONFIGURABLE_TOOLSETS:
+            ts_tools = set(resolve_toolset(ts_key))
+            if ts_tools and ts_tools.issubset(all_tool_names):
+                enabled_toolsets.add(ts_key)
 
     # Plugin toolsets: enabled by default unless explicitly disabled.
     # A plugin toolset is "known" for a platform once `hermes tools`
@@ -437,15 +448,21 @@ def _save_platform_tools(config: dict, platform: str, enabled_toolset_keys: Set[
     plugin_keys = _get_plugin_toolset_keys()
     configurable_keys |= plugin_keys
 
+    # Also exclude platform default toolsets (hermes-cli, hermes-telegram, etc.)
+    # These are "super" toolsets that resolve to ALL tools, so preserving them
+    # would silently override the user's unchecked selections on the next read.
+    platform_default_keys = {p["default_toolset"] for p in PLATFORMS.values()}
+
     # Get existing toolsets for this platform
     existing_toolsets = config.get("platform_toolsets", {}).get(platform, [])
     if not isinstance(existing_toolsets, list):
         existing_toolsets = []
 
-    # Preserve any entries that are NOT configurable toolsets (i.e. MCP server names)
+    # Preserve any entries that are NOT configurable toolsets and NOT platform
+    # defaults (i.e. only MCP server names should be preserved)
     preserved_entries = {
         entry for entry in existing_toolsets
-        if entry not in configurable_keys
+        if entry not in configurable_keys and entry not in platform_default_keys
     }
 
     # Merge preserved entries with new enabled toolsets
diff --git a/tests/hermes_cli/test_tools_config.py b/tests/hermes_cli/test_tools_config.py
index 4aee5947a79..676305dbd7b 100644
--- a/tests/hermes_cli/test_tools_config.py
+++ b/tests/hermes_cli/test_tools_config.py
@@ -100,3 +100,107 @@ def test_save_platform_tools_handles_invalid_existing_config():
 
     saved_toolsets = config["platform_toolsets"]["cli"]
     assert "web" in saved_toolsets
+
+
+def test_save_platform_tools_does_not_preserve_platform_default_toolsets():
+    """Platform default toolsets (hermes-cli, hermes-telegram, etc.) must NOT
+    be preserved across saves.
+
+    These "super" toolsets resolve to ALL tools, so if they survive in the
+    config, they silently override any tools the user unchecked. Previously,
+    the preserve filter only excluded configurable toolset keys (web, browser,
+    terminal, etc.) and treated platform defaults as unknown custom entries
+    (like MCP server names), causing them to be kept unconditionally.
+
+    Regression test: user unchecks image_gen and homeassistant via
+    ``hermes tools``, but hermes-cli stays in the config and re-enables
+    everything on the next read.
+    """
+    config = {
+        "platform_toolsets": {
+            "cli": [
+                "browser", "clarify", "code_execution", "cronjob",
+                "delegation", "file", "hermes-cli",  # <-- the culprit
+                "memory", "session_search", "skills", "terminal",
+                "todo", "tts", "vision", "web",
+            ]
+        }
+    }
+
+    # User unchecks image_gen, homeassistant, moa — keeps the rest
+    new_selection = {
+        "browser", "clarify", "code_execution", "cronjob",
+        "delegation", "file", "memory", "session_search",
+        "skills", "terminal", "todo", "tts", "vision", "web",
+    }
+
+    with patch("hermes_cli.tools_config.save_config"):
+        _save_platform_tools(config, "cli", new_selection)
+
+    saved = config["platform_toolsets"]["cli"]
+
+    # hermes-cli must NOT survive — it's a platform default, not an MCP server
+    assert "hermes-cli" not in saved
+
+    # The individual toolset keys the user selected must be present
+    assert "web" in saved
+    assert "terminal" in saved
+    assert "browser" in saved
+
+    # Tools the user unchecked must NOT be present
+    assert "image_gen" not in saved
+    assert "homeassistant" not in saved
+    assert "moa" not in saved
+
+
+def test_save_platform_tools_does_not_preserve_hermes_telegram():
+    """Same bug for Telegram — hermes-telegram must not be preserved."""
+    config = {
+        "platform_toolsets": {
+            "telegram": [
+                "browser", "file", "hermes-telegram", "terminal", "web",
+            ]
+        }
+    }
+
+    new_selection = {"browser", "file", "terminal", "web"}
+
+    with patch("hermes_cli.tools_config.save_config"):
+        _save_platform_tools(config, "telegram", new_selection)
+
+    saved = config["platform_toolsets"]["telegram"]
+    assert "hermes-telegram" not in saved
+    assert "web" in saved
+
+
+def test_save_platform_tools_still_preserves_mcp_with_platform_default_present():
+    """MCP server names must still be preserved even when platform defaults
+    are being stripped out."""
+    config = {
+        "platform_toolsets": {
+            "cli": [
+                "web", "terminal", "hermes-cli", "my-mcp-server", "github-tools",
+            ]
+        }
+    }
+
+    new_selection = {"web", "browser"}
+
+    with patch("hermes_cli.tools_config.save_config"):
+        _save_platform_tools(config, "cli", new_selection)
+
+    saved = config["platform_toolsets"]["cli"]
+
+    # MCP servers preserved
+    assert "my-mcp-server" in saved
+    assert "github-tools" in saved
+
+    # Platform default stripped
+    assert "hermes-cli" not in saved
+
+    # User selections present
+    assert "web" in saved
+    assert "browser" in saved
+
+    # Deselected configurable toolset removed
+    assert "terminal" not in saved