exa-mcp-server ignores --tools option after update: how to select enabled tools?

Question

After the July 2025 release, exa-mcp-server no longer honors --tools=web_search_exa,... in the mcp.json args, and the newer enabledTools array also appears to be ignored; all tools get exposed. How do you limit which tools the server enables, and is this regression fixed?

Originally asked on GitHub: https://github.com/exa-labs/exa-mcp-server/issues/48

AgentArmorHQ team · Accepted Answer

Fixed in exa-mcp-server 3.0.8. Per the maintainer (comment from 2025-11-06), using multiple or all 7 tools works again starting with 3.0.8; a commenter suspected the old `--tools` flag broke when the server moved to Smithery CLI handling and that the docs were not updated.

With the npm package, pass a single `tools=` CLI argument listing the tools comma-separated:

```json
{
  "mcpServers": {
    "exa": {
      "command": "npx",
      "args": [
        "-y",
        "exa-mcp-server",
        "tools=get_code_context_exa,web_search_exa,company_research_exa,crawling_exa,linkedin_search_exa,deep_researcher_start,deep_researcher_check"
      ],
      "env": {
        "EXA_API_KEY": "your-api-key-here"
      }
    }
  }
}
```

For the remote MCP endpoint, the same list goes in the URL:

```json
{
  "mcpServers": {
    "exa": {
      "type": "http",
      "url": "https://mcp.exa.ai/mcp?tools=web_search_exa,get_code_context_exa,crawling_exa,company_research_exa,linkedin_search_exa,deep_researcher_start,deep_researcher_check",
      "headers": {}
    }
  }
}
```

Before 3.0.8, a workaround confirmed in the thread: pass `enabledTools` as a CLI argument instead of the `--tools` flag, with quotes escaped in JSON:

```json
"args": ["-y", "exa-mcp-server", "enabledTools=[\"web_search_exa\",\"crawling_exa\"]"]
```

The API key still works via the `EXA_API_KEY` environment variable or the `exaApiKey` CLI option. Use the current tool names (e.g. `web_search_exa`, `crawling_exa`, `deep_researcher_start`, `deep_researcher_check`) as shown in the maintainer's list.

General advice: keep the API key in the `env` block rather than in `args` so it doesn't appear in process listings or logs.

AgentArmorHQ team · Answer

**What a GitHub user tried on GitHub** (Didn't work)

Reporter configured `--tools=web_search_exa,research_paper_search,company_research,crawling` in the mcp.json args and also tried an `enabledTools` array in the config; all tools were still exposed.

Source: https://github.com/exa-labs/exa-mcp-server/issues/48

AgentArmorHQ team · Answer

**What @stanley2058 tried on GitHub** (Worked)

Commenter ran `npx exa-mcp-server enabledTools='["web_search_exa","crawling_exa"]'` and the debug log showed only those tools enabled; in JSON configs the quotes must be escaped. Another commenter later confirmed this solution works.

Source: https://github.com/exa-labs/exa-mcp-server/issues/48#issuecomment-3462407278

AgentArmorHQ team · Answer

**What @theishangoswami tried on GitHub** (Worked)

Maintainer stated the issue is fixed in npm package 3.0.8 and provided the new `tools=` CLI argument (or `?tools=` URL parameter for the remote MCP) listing all 7 tool names.

Source: https://github.com/exa-labs/exa-mcp-server/issues/48#issuecomment-3499887680

exa-mcp-server ignores --tools option after update: how to select enabled tools?

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exa-mcp-server ignores --tools option after update: how to select enabled tools?

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