---
title: Claude Code Not Finding MCP Tools? Check These Settings
description: A custom ANTHROPIC_BASE_URL turned Claude Code tool search off; --tools "" removed it. First-request sizes per setting, and quick checks when tools go missing.
canonical: https://spiritroom.app/blog/claude-code-mcp-tools-not-found/
published: 2026-10-21
updated: 2026-10-21
---

> Markdown version of https://spiritroom.app/blog/claude-code-mcp-tools-not-found/ for agents. Index: /llms.txt

[Blog](/blog/) / [How agents load MCP tools](/guides/how-agents-load-mcp-tools/)

# Claude Code can't see your MCP tools? Check the proxy and --tools settings first

For the basics (adding a server, scopes, auth) see the official docs. This page covers only the gotchas we hit, with numbers.

Leonid Bugaev · Published 21 Oct 2026

**TL;DR**

- **Default:** tool search on; 99 MCP tools added only 1,715 tokens up front (22,791 total).
- **Custom ANTHROPIC\_BASE\_URL** (proxy or gateway): tool search off, all 99 definitions preloaded: 143,357 tokens.
- **ENABLE\_TOOL\_SEARCH=true** turned it back on behind the proxy: 22,446.
- **`--tools ""`** removed ToolSearch itself: 110,998 tokens, and the env var couldn't restore it. Use `--tools "ToolSearch"` to keep it.
- **Untrusted folders and other apps:** some drop project servers silently. Check that the server is listed before debugging the model.
[What each setting did](#matrix)[Quick checks](#checks)[When it's the model, not the setup](#model)[How we measured](#how-we-measured)[FAQ](#faq)

Basics first: [Claude Code MCP documentation](https://code.claude.com/docs/en/mcp).

## What each setting did

Claude Code 2.1.301 with a 99-tool mock server, prompt “say hi”, first-request input tokens:

| Config | First request | Tool search |
| --- | --- | --- |
| Default | 22,791 | on |
| `--setting-sources ""` | 18,102 | on |
| `--tools "ToolSearch"` | 5,787 | on |
| `--tools ""` | 110,998 | **off** |
| `--tools ""` + `ENABLE_TOOL_SEARCH=true` | 111,000 | **off** |
| Custom `ANTHROPIC_BASE_URL` | 143,357 | **off** |
| Custom base URL + `ENABLE_TOOL_SEARCH=true` | 22,446 | on |

Default

*22,791*

Custom base URL

*143,357*

“Off” means every MCP tool definition was in every request. Your tools are all visible then, but heavy; with “on”, they're visible by name only. See [Claude Code tool search, seen from the wire](/blog/claude-code-tool-search-explained/).

**Agents still not finding your tools?**

We check how Claude Code and the other agent apps your users run load and find your MCP tools, and why they miss them.

[Test your MCP →](/#contact)

## Quick checks

1. Is the server connected? Check the app's MCP status before anything else.
2. Any custom `ANTHROPIC_BASE_URL`, proxy or gateway? Try `ENABLE_TOOL_SEARCH=true`.
3. Restricting built-in tools? Keep `ToolSearch` in the list.
4. Comparing runs or running evals? Measure the first request against a default run, so your lab matches your users.
5. Other apps: a project server in an untrusted folder was dropped silently by Grok Build in headless mode.

## When it's the model, not the setup

If the tools are listed but the agent doesn't pick them, it's discovery: the model chose from names, or the user didn't name your product. See [when the agent doesn't recognise your server](/blog/agent-does-not-recognise-mcp-server/) and [name tools the way users talk](/blog/mcp-tool-naming-for-agent-search/).

**Go deeper:** [Capture what your agent sends](/blog/capture-agent-model-traffic/), [How Codex finds MCP tools](/blog/how-codex-finds-mcp-tools/), [MCP tool-list token calculator](/tools/mcp-token-cost/).

Back to [how agents load MCP tools](/guides/how-agents-load-mcp-tools/).

## How we measured

- Claude Code 2.1.301, 16 Oct 2026, a mock serving a recorded 99-tool list, single runs per config, first-request input from the app's own usage; tool search state confirmed from captured request bodies and debug logs.
- Single runs: settings behaviour, not rates. Versions change; re-check after updates.

## FAQ

### Why does Claude Code not find my MCP tools?

First rule out setup: is the server connected and listed? Then check settings that change tool loading: a custom ANTHROPIC\_BASE\_URL turned tool search off in our tests, and --tools "" removed ToolSearch. If tools load but aren't chosen, look at names and descriptions.

### Does a proxy or gateway change Claude Code's tool loading?

In our test, yes: with a custom ANTHROPIC\_BASE\_URL, Claude Code preloaded all 99 MCP tool definitions (143,357 tokens in the first request) instead of using tool search. Setting ENABLE\_TOOL\_SEARCH=true restored it.

### How do I keep tool search when restricting built-in tools?

Include it: --tools "ToolSearch" kept tool search on (5,787 tokens in our test), while --tools "" removed it.

**Agents still not finding your tools?**

We check how Claude Code and the other agent apps your users run load and find your MCP tools, and why they miss them.

[Test your MCP →](/#contact)

## Keep reading

- Up[How agent apps load MCP tools: what the model sees (guide)](/guides/how-agents-load-mcp-tools/)
- Related[Claude Code tool search, seen from the wire: the model picks your tool from its name](/blog/claude-code-tool-search-explained/)
- Related[When the agent doesn't know your MCP server is the right tool (“Which product do you mean?”)](/blog/agent-does-not-recognise-mcp-server/)