diff --git a/agent/prompt_builder.py b/agent/prompt_builder.py
index 4ce84473f5..8dc3124ba9 100644
--- a/agent/prompt_builder.py
+++ b/agent/prompt_builder.py
@@ -330,28 +330,34 @@ def build_skills_system_prompt(
     # Each entry: (skill_name, description)
     # Supports sub-categories: skills/mlops/training/axolotl/SKILL.md
     # -> category "mlops/training", skill "axolotl"
+    # Load disabled skill names once for the entire scan
+    try:
+        from tools.skills_tool import _get_disabled_skill_names
+        disabled = _get_disabled_skill_names()
+    except Exception:
+        disabled = set()
+
     skills_by_category: dict[str, list[tuple[str, str]]] = {}
     for skill_file in skills_dir.rglob("SKILL.md"):
-        is_compatible, _, desc = _parse_skill_file(skill_file)
+        is_compatible, frontmatter, desc = _parse_skill_file(skill_file)
         if not is_compatible:
             continue
-        # Skip skills whose conditional activation rules exclude them
-        conditions = _read_skill_conditions(skill_file)
-        if not _skill_should_show(conditions, available_tools, available_toolsets):
-            continue
         rel_path = skill_file.relative_to(skills_dir)
         parts = rel_path.parts
         if len(parts) >= 2:
-            # Category is everything between skills_dir and the skill folder
-            # e.g. parts = ("mlops", "training", "axolotl", "SKILL.md")
-            #   → category = "mlops/training", skill_name = "axolotl"
-            # e.g. parts = ("github", "github-auth", "SKILL.md")
-            #   → category = "github", skill_name = "github-auth"
             skill_name = parts[-2]
             category = "/".join(parts[:-2]) if len(parts) > 2 else parts[0]
         else:
             category = "general"
             skill_name = skill_file.parent.name
+        # Respect user's disabled skills config
+        fm_name = frontmatter.get("name", skill_name)
+        if fm_name in disabled or skill_name in disabled:
+            continue
+        # Skip skills whose conditional activation rules exclude them
+        conditions = _read_skill_conditions(skill_file)
+        if not _skill_should_show(conditions, available_tools, available_toolsets):
+            continue
         skills_by_category.setdefault(category, []).append((skill_name, desc))
 
     if not skills_by_category:
diff --git a/agent/skill_commands.py b/agent/skill_commands.py
index 67315ee8df..b266ad251c 100644
--- a/agent/skill_commands.py
+++ b/agent/skill_commands.py
@@ -157,9 +157,10 @@ def scan_skill_commands() -> Dict[str, Dict[str, Any]]:
     global _skill_commands
     _skill_commands = {}
     try:
-        from tools.skills_tool import SKILLS_DIR, _parse_frontmatter, skill_matches_platform
+        from tools.skills_tool import SKILLS_DIR, _parse_frontmatter, skill_matches_platform, _get_disabled_skill_names
         if not SKILLS_DIR.exists():
             return _skill_commands
+        disabled = _get_disabled_skill_names()
         for skill_md in SKILLS_DIR.rglob("SKILL.md"):
             if any(part in ('.git', '.github', '.hub') for part in skill_md.parts):
                 continue
@@ -170,6 +171,9 @@ def scan_skill_commands() -> Dict[str, Dict[str, Any]]:
                 if not skill_matches_platform(frontmatter):
                     continue
                 name = frontmatter.get('name', skill_md.parent.name)
+                # Respect user's disabled skills config
+                if name in disabled:
+                    continue
                 description = frontmatter.get('description', '')
                 if not description:
                     for line in body.strip().split('\n'):
diff --git a/tests/agent/test_prompt_builder.py b/tests/agent/test_prompt_builder.py
index 1de37efbe5..07c8da1891 100644
--- a/tests/agent/test_prompt_builder.py
+++ b/tests/agent/test_prompt_builder.py
@@ -309,6 +309,35 @@ class TestBuildSkillsSystemPrompt:
         assert "imessage" in result
         assert "Send iMessages" in result
 
+    def test_excludes_disabled_skills(self, monkeypatch, tmp_path):
+        """Skills in the user's disabled list should not appear in the system prompt."""
+        monkeypatch.setenv("HERMES_HOME", str(tmp_path))
+        skills_dir = tmp_path / "skills" / "tools"
+        skills_dir.mkdir(parents=True)
+
+        enabled_skill = skills_dir / "web-search"
+        enabled_skill.mkdir()
+        (enabled_skill / "SKILL.md").write_text(
+            "---\nname: web-search\ndescription: Search the web\n---\n"
+        )
+
+        disabled_skill = skills_dir / "old-tool"
+        disabled_skill.mkdir()
+        (disabled_skill / "SKILL.md").write_text(
+            "---\nname: old-tool\ndescription: Deprecated tool\n---\n"
+        )
+
+        from unittest.mock import patch
+
+        with patch(
+            "tools.skills_tool._get_disabled_skill_names",
+            return_value={"old-tool"},
+        ):
+            result = build_skills_system_prompt()
+
+        assert "web-search" in result
+        assert "old-tool" not in result
+
     def test_includes_setup_needed_skills(self, monkeypatch, tmp_path):
         monkeypatch.setenv("HERMES_HOME", str(tmp_path))
         monkeypatch.delenv("MISSING_API_KEY_XYZ", raising=False)
diff --git a/tests/agent/test_skill_commands.py b/tests/agent/test_skill_commands.py
index c024461380..f6a114db67 100644
--- a/tests/agent/test_skill_commands.py
+++ b/tests/agent/test_skill_commands.py
@@ -85,6 +85,21 @@ class TestScanSkillCommands:
             result = scan_skill_commands()
         assert "/generic-tool" in result
 
+    def test_excludes_disabled_skills(self, tmp_path):
+        """Disabled skills should not register slash commands."""
+        with (
+            patch("tools.skills_tool.SKILLS_DIR", tmp_path),
+            patch(
+                "tools.skills_tool._get_disabled_skill_names",
+                return_value={"disabled-skill"},
+            ),
+        ):
+            _make_skill(tmp_path, "enabled-skill")
+            _make_skill(tmp_path, "disabled-skill")
+            result = scan_skill_commands()
+        assert "/enabled-skill" in result
+        assert "/disabled-skill" not in result
+
 
 class TestBuildPreloadedSkillsPrompt:
     def test_builds_prompt_for_multiple_named_skills(self, tmp_path):