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Luca Moretti
Luca Moretti

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How to Secure Your MCP Server's API Keys (With Working Demo)

#mcp #security #tutorial #ai

The Problem Every MCP Developer Ignores

You build an MCP server. It needs a GitHub token. Maybe an OpenAI key. Where do they go?

{
  "mcpServers": {
    "my-server": {
      "command": "node",
      "args": ["server.js"],
      "env": {
        "GITHUB_TOKEN": "ghp_XXXXXXXXXXXX",
        "OPENAI_API_KEY": "sk-XXXXXXXXXXXX"
      }
    }
  }
}
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Plaintext. In a JSON file. On disk. Possibly committed to git.

This is how most MCP servers handle secrets today. And it's a ticking time bomb.

A Better Way: Encrypted Vault + Runtime Decryption

I built a demo MCP server that does it differently. Instead of reading secrets from env vars, it pulls them from Janee — an encrypted vault designed for MCP servers.

The flow:

Claude Desktop → MCP Protocol → Your Server → Janee Vault → API Call
                                                   ↑
                                         AES-256-GCM encrypted
                                         Decrypted only at runtime
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No plaintext secrets on disk. Ever.

Try It Yourself (5 minutes) 

git clone https://github.com/lucamorettibuilds/janee-mcp-demo
cd janee-mcp-demo
npm install

# Set up the encrypted vault
npx janee init          # Creates encrypted vault
npx janee add github    # Stores your GitHub token (encrypted)
npx janee add openai    # Stores your OpenAI key (encrypted)

# Run it
export JANEE_MASTER_PASSWORD="your-password"
npm start
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The server exposes three MCP tools:

  • github_create_issue — creates GitHub issues using vault credentials
  • openai_complete — calls OpenAI using vault credentials
  • list_secrets — shows what's in the vault (names only, never values)

How the Code Works

The secret sauce is a tiny integration layer (src/secrets.js):

import { execSync } from "child_process";

export async function getSecret(service, field) {
  try {
    const result = execSync(
      `npx janee get ${service} ${field} 2>/dev/null`,
      { encoding: "utf-8", env: { ...process.env } }
    ).trim();
    return result || null;
  } catch {
    return null;
  }
}
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Then in your MCP tool handler, instead of process.env.GITHUB_TOKEN:

const token = await getSecret("github", "token");
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That's it. The secret is decrypted from the vault at runtime, used for the API call, and never persisted in memory longer than needed.

Claude Desktop Config 

{
  "mcpServers": {
    "janee-demo": {
      "command": "node",
      "args": ["/path/to/janee-mcp-demo/src/server.js"],
      "env": {
        "JANEE_MASTER_PASSWORD": "your-master-password"
      }
    }
  }
}
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Notice: one password protects all your API keys. No more scatter-shot env vars.

Why Not Just Use .env Files?

.env files Janee vault
Storage Plaintext AES-256-GCM encrypted
Access control None Session-based with TTL
Rotation Manual find-and-replace janee add service (overwrites)
Audit None Built-in logging
Git safety Needs .gitignore discipline Vault file is safe to commit

Adding Your Own Services

The demo ships with GitHub and OpenAI, but you can add anything:

npx janee add stripe
npx janee add anthropic  
npx janee add postgres
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Then use getSecret("stripe", "api_key") in your tool handler.

Get the Code

If you're building MCP servers, give your secrets the respect they deserve. ⭐ Janee if it's useful.

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