diff --git a/src/mcp_codebase_index/server.py b/src/mcp_codebase_index/server.py
index 72126da..50c4f20 100644
--- a/src/mcp_codebase_index/server.py
+++ b/src/mcp_codebase_index/server.py
@@ -28,12 +28,14 @@
 
 from __future__ import annotations
 
+import argparse
 import fnmatch
 import json
 import os
 import sys
 import pickle
 import time
+import tomllib
 import traceback
 
 from mcp.server import Server
@@ -66,6 +68,10 @@
 _tool_call_counts: dict[str, int] = {}
 _total_chars_returned: int = 0
 
+# Tool toggling
+PROTECTED_TOOLS: frozenset[str] = frozenset({"reindex", "get_usage_stats"})
+_disabled_tools: set[str] = set()
+
 # Realistic estimate of what % of codebase you'd need to read without the indexer
 _TOOL_COST_MULTIPLIERS: dict[str, float] = {
     "get_project_summary": 0.10,
@@ -88,6 +94,78 @@
 }
 
 
+_ALL_TOOL_NAMES: frozenset[str] = frozenset()  # set after TOOLS is defined
+
+
+def _load_disabled_tools_from_config(project_root: str) -> set[str]:
+    """Read `.mcp-codebase-index.toml` and return the set of disabled tool names."""
+    config_path = os.path.join(project_root, ".mcp-codebase-index.toml")
+    if not os.path.isfile(config_path):
+        return set()
+    try:
+        with open(config_path, "rb") as f:
+            data = tomllib.load(f)
+    except Exception as exc:
+        print(
+            f"[mcp-codebase-index] Warning: failed to parse {config_path}: {exc}",
+            file=sys.stderr,
+        )
+        return set()
+    raw = data.get("disabled_tools")
+    if raw is None:
+        return set()
+    if not isinstance(raw, list) or not all(isinstance(s, str) for s in raw):
+        print(
+            "[mcp-codebase-index] Warning: disabled_tools must be a list of strings, ignoring",
+            file=sys.stderr,
+        )
+        return set()
+    return {s.strip() for s in raw if s.strip()}
+
+
+def _init_disabled_tools(
+    cli_disabled: list[str] | None = None,
+    *,
+    project_root: str | None = None,
+) -> None:
+    """Union CLI + config disabled tools, strip protected, warn about unknowns."""
+    global _disabled_tools
+    merged: set[str] = set()
+
+    if cli_disabled:
+        merged.update(cli_disabled)
+
+    root = project_root or os.environ.get("PROJECT_ROOT", os.getcwd())
+    merged |= _load_disabled_tools_from_config(root)
+
+    # Warn about protected tools that a user tried to disable
+    protected_requested = merged & PROTECTED_TOOLS
+    if protected_requested:
+        print(
+            f"[mcp-codebase-index] Warning: cannot disable protected tools: "
+            f"{', '.join(sorted(protected_requested))}",
+            file=sys.stderr,
+        )
+    merged -= PROTECTED_TOOLS
+
+    # Warn about unknown tool names
+    unknown = merged - _ALL_TOOL_NAMES
+    if unknown:
+        print(
+            f"[mcp-codebase-index] Warning: unknown tools ignored: "
+            f"{', '.join(sorted(unknown))}",
+            file=sys.stderr,
+        )
+    merged &= _ALL_TOOL_NAMES
+
+    _disabled_tools = merged
+    if _disabled_tools:
+        print(
+            f"[mcp-codebase-index] Disabled tools: {', '.join(sorted(_disabled_tools))}",
+            file=sys.stderr,
+        )
+
+
 def _format_result(value: object) -> str:
     """Format a query result as readable text."""
     if isinstance(value, str):
@@ -648,6 +726,9 @@ def _maybe_incremental_update() -> None:
     ),
 ]
 
+# Now that TOOLS is defined, set the real _ALL_TOOL_NAMES
+_ALL_TOOL_NAMES = frozenset(t.name for t in TOOLS)
+
 
 # ---------------------------------------------------------------------------
 # MCP handlers
@@ -656,6 +737,8 @@ def _maybe_incremental_update() -> None:
 
 @server.list_tools()
 async def list_tools() -> list[Tool]:
+    if _disabled_tools:
+        return [t for t in TOOLS if t.name not in _disabled_tools]
     return TOOLS
 
 
@@ -663,6 +746,13 @@ async def list_tools() -> list[Tool]:
 async def call_tool(name: str, arguments: dict) -> list[types.TextContent]:
     global _query_fns, _total_chars_returned
 
+    # Reject disabled tools before doing any work
+    if name in _disabled_tools:
+        return [TextContent(
+            type="text",
+            text=f"Error: tool '{name}' is disabled.",
+        )]
+
     # Track tool call counts (including reindex/stats themselves)
     _tool_call_counts[name] = _tool_call_counts.get(name, 0) + 1
 
@@ -787,7 +877,8 @@ async def call_tool(name: str, arguments: dict) -> list[types.TextContent]:
 # ---------------------------------------------------------------------------
 
 
-async def main():
+async def main(cli_disabled: list[str] | None = None):
+    _init_disabled_tools(cli_disabled)
     async with stdio_server() as (read_stream, write_stream):
         await server.run(
             read_stream,
@@ -800,7 +891,20 @@ def main_sync():
     """Synchronous entry point for console_scripts."""
     import asyncio
 
-    asyncio.run(main())
+    parser = argparse.ArgumentParser(description="MCP codebase index server")
+    parser.add_argument(
+        "--disabled-tools",
+        type=lambda s: [t.strip() for t in s.split(",") if t.strip()],
+        default=None,
+        help="Comma-separated list of tool names to disable (e.g. search_codebase,get_call_chain)",
+    )
+    args, unknown = parser.parse_known_args()
+    if unknown:
+        print(
+            f"[mcp-codebase-index] Ignoring unknown arguments: {' '.join(unknown)}",
+            file=sys.stderr,
+        )
+    asyncio.run(main(cli_disabled=args.disabled_tools))
 
 
 if __name__ == "__main__":
diff --git a/tests/test_tool_toggle.py b/tests/test_tool_toggle.py
new file mode 100644
index 0000000..d5ae297
--- /dev/null
+++ b/tests/test_tool_toggle.py
@@ -0,0 +1,227 @@
+"""Tests for the tool toggling feature (--disabled-tools + TOML config)."""
+
+import asyncio
+
+import pytest
+
+import mcp_codebase_index.server as srv
+
+
+@pytest.fixture(autouse=True)
+def _reset_toggle_state():
+    """Reset the disabled-tools set and related state before each test."""
+    srv._disabled_tools = set()
+    yield
+    srv._disabled_tools = set()
+
+
+# ---------------------------------------------------------------------------
+# _load_disabled_tools_from_config
+# ---------------------------------------------------------------------------
+
+
+class TestLoadDisabledToolsFromConfig:
+    def test_no_config_file(self, tmp_path):
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_valid_config(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text(
+            'disabled_tools = ["search_codebase", "get_call_chain"]\n'
+        )
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == {"search_codebase", "get_call_chain"}
+
+    def test_empty_list(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text("disabled_tools = []\n")
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_invalid_type_not_list(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text('disabled_tools = "search_codebase"\n')
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_invalid_type_list_of_non_strings(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text("disabled_tools = [1, 2]\n")
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_malformed_toml(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text("not valid toml [[[")
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_missing_key(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text("[other]\nfoo = 1\n")
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == set()
+
+    def test_whitespace_in_values_stripped(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text(
+            'disabled_tools = [" search_codebase ", "get_call_chain "]\n'
+        )
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == {"search_codebase", "get_call_chain"}
+
+    def test_blank_strings_filtered(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text(
+            'disabled_tools = ["search_codebase", " ", ""]\n'
+        )
+        result = srv._load_disabled_tools_from_config(str(tmp_path))
+        assert result == {"search_codebase"}
+
+
+# ---------------------------------------------------------------------------
+# _init_disabled_tools
+# ---------------------------------------------------------------------------
+
+
+class TestInitDisabledTools:
+    def test_cli_only(self, tmp_path):
+        srv._init_disabled_tools(["search_codebase"], project_root=str(tmp_path))
+        assert srv._disabled_tools == {"search_codebase"}
+
+    def test_config_only(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text(
+            'disabled_tools = ["get_call_chain"]\n'
+        )
+        srv._init_disabled_tools(None, project_root=str(tmp_path))
+        assert srv._disabled_tools == {"get_call_chain"}
+
+    def test_union_of_cli_and_config(self, tmp_path):
+        (tmp_path / ".mcp-codebase-index.toml").write_text(
+            'disabled_tools = ["get_call_chain"]\n'
+        )
+        srv._init_disabled_tools(["search_codebase"], project_root=str(tmp_path))
+        assert srv._disabled_tools == {"search_codebase", "get_call_chain"}
+
+    def test_protected_tools_cannot_be_disabled(self, tmp_path):
+        srv._init_disabled_tools(["reindex", "get_usage_stats", "search_codebase"],
+                                 project_root=str(tmp_path))
+        assert "reindex" not in srv._disabled_tools
+        assert "get_usage_stats" not in srv._disabled_tools
+        assert "search_codebase" in srv._disabled_tools
+
+    def test_unknown_tools_ignored(self, tmp_path):
+        srv._init_disabled_tools(["not_a_real_tool", "search_codebase"],
+                                 project_root=str(tmp_path))
+        assert "not_a_real_tool" not in srv._disabled_tools
+        assert "search_codebase" in srv._disabled_tools
+
+    def test_empty_cli_list(self, tmp_path):
+        srv._init_disabled_tools([], project_root=str(tmp_path))
+        assert srv._disabled_tools == set()
+
+    def test_none_cli_no_config(self, tmp_path):
+        srv._init_disabled_tools(None, project_root=str(tmp_path))
+        assert srv._disabled_tools == set()
+
+
+# ---------------------------------------------------------------------------
+# list_tools filtering
+# ---------------------------------------------------------------------------
+
+
+class TestListToolsFiltering:
+    def test_no_disabled_returns_all(self):
+        srv._disabled_tools = set()
+        tools = asyncio.run(srv.list_tools())
+        assert len(tools) == len(srv.TOOLS)
+
+    def test_disabled_tools_excluded(self):
+        srv._disabled_tools = {"search_codebase", "get_call_chain"}
+        tools = asyncio.run(srv.list_tools())
+        names = {t.name for t in tools}
+        assert "search_codebase" not in names
+        assert "get_call_chain" not in names
+        assert len(tools) == len(srv.TOOLS) - 2
+
+    def test_protected_always_present(self):
+        srv._disabled_tools = {"search_codebase"}
+        tools = asyncio.run(srv.list_tools())
+        names = {t.name for t in tools}
+        assert "reindex" in names
+        assert "get_usage_stats" in names
+
+
+# ---------------------------------------------------------------------------
+# call_tool guard
+# ---------------------------------------------------------------------------
+
+
+class TestCallToolGuard:
+    def test_disabled_tool_returns_error(self):
+        srv._disabled_tools = {"search_codebase"}
+        result = asyncio.run(srv.call_tool("search_codebase", {"pattern": "foo"}))
+        assert len(result) == 1
+        assert "disabled" in result[0].text
+        assert "search_codebase" in result[0].text
+
+    def test_disabled_tool_not_counted(self):
+        srv._tool_call_counts.clear()
+        srv._disabled_tools = {"search_codebase"}
+        asyncio.run(srv.call_tool("search_codebase", {"pattern": "foo"}))
+        assert "search_codebase" not in srv._tool_call_counts
+
+    def test_enabled_tool_not_blocked(self, monkeypatch):
+        """An enabled tool should proceed past the guard (we mock _ensure_index)."""
+        srv._disabled_tools = set()
+        srv._tool_call_counts.clear()
+        # Prevent actual indexing
+        monkeypatch.setattr(srv, "_ensure_index", lambda: None)
+        monkeypatch.setattr(srv, "_maybe_incremental_update", lambda: None)
+        monkeypatch.setattr(srv, "_query_fns", {
+            "get_project_summary": lambda: "mock summary",
+        })
+        result = asyncio.run(srv.call_tool("get_project_summary", {}))
+        assert result[0].text == "mock summary"
+        assert srv._tool_call_counts.get("get_project_summary") == 1
+
+
+# ---------------------------------------------------------------------------
+# CLI argument parsing (main_sync integration)
+# ---------------------------------------------------------------------------
+
+
+class TestCliParsing:
+    def _parse(self, argv: list[str]) -> tuple:
+        """Run the same argparse logic as main_sync with custom argv."""
+        import argparse
+
+        parser = argparse.ArgumentParser(description="MCP codebase index server")
+        parser.add_argument(
+            "--disabled-tools",
+            type=lambda s: [t.strip() for t in s.split(",") if t.strip()],
+            default=None,
+            help="Comma-separated list of tool names to disable",
+        )
+        return parser.parse_known_args(argv)
+
+    def test_disabled_tools_parsed(self):
+        args, unknown = self._parse(["--disabled-tools", "search_codebase,get_call_chain"])
+        assert args.disabled_tools == ["search_codebase", "get_call_chain"]
+        assert unknown == []
+
+    def test_disabled_tools_with_spaces(self):
+        args, _ = self._parse(["--disabled-tools", " search_codebase , get_call_chain "])
+        assert args.disabled_tools == ["search_codebase", "get_call_chain"]
+
+    def test_no_disabled_tools_flag(self):
+        args, unknown = self._parse([])
+        assert args.disabled_tools is None
+        assert unknown == []
+
+    def test_unknown_args_not_fatal(self):
+        """parse_known_args must not raise SystemExit on unknown flags."""
+        args, unknown = self._parse(["--some-future-flag", "value"])
+        assert args.disabled_tools is None
+        assert "--some-future-flag" in unknown
+
+    def test_unknown_args_coexist_with_disabled_tools(self):
+        args, unknown = self._parse([
+            "--disabled-tools", "search_codebase",
+            "--unknown-flag",
+        ])
+        assert args.disabled_tools == ["search_codebase"]
+        assert "--unknown-flag" in unknown