MCP Secrets Management

The core problem

MCP servers need API keys and credentials to function. Storing them in plaintext in settings.json or .mcp.json creates a real risk: accidental commit to Git, exposure in logs, or lateral movement after a compromise. The absolute rule is that secrets must never appear in versioned files.

Three approaches depending on context

Approach 1: OS Keychain (recommended)

The secret is encrypted at rest by the OS and accessible only to authorized processes. The MCP configuration exposes only a retrieval command, never the value.

# macOS: store a GitHub token
security add-generic-password \
  -a "claude-mcp" -s "github-token" \
  -w "ghp_your_token_here"

{
  "mcpServers": {
    "github": {
      "command": "bash",
      "args": ["-c", "GITHUB_TOKEN=$(security find-generic-password -s 'github-token' -w) npx @github/mcp-server"]
    }
  }
}

Linux: use secret-tool (libsecret, GNOME Keyring or KWallet) with the same wrapper script logic.

Approach 2: .env + .gitignore

Simple and sufficient for solo use or a small team with good discipline.

# Create the secrets file
cat > ~/.claude/.env << EOF
GITHUB_TOKEN=ghp_your_token
OPENAI_KEY=sk-your_key
EOF
chmod 600 ~/.claude/.env   # Restrictive permissions
echo ".env" >> ~/.claude/.gitignore

In the MCP config, reference with "${GITHUB_TOKEN}" in the env field. Claude Code resolves environment variables at server startup.

Template for teams: commit mcp-config.template.json with placeholders, generate the real file via envsubst. Never commit the generated file.

Approach 3: Secret Vaults (enterprise)

HashiCorp Vault, AWS Secrets Manager, or 1Password CLI enable automated rotation, centralized auditing, and granular access control. The principle remains identical: a wrapper script retrieves the secret at runtime and exports it as an environment variable before launching the MCP server.

# HashiCorp Vault
export GITHUB_TOKEN=$(vault kv get -field=token secret/claude/github)
npx @github/mcp-server

What to never do

Hardcode a token directly in the command or args value of a versioned MCP server. Even in a private repo, secrets in plaintext in Git remain in the history even after deletion and can be exposed by a git log or unauthorized access.

A pre-commit hook that scans for token patterns (ghp_, sk-, Bearer ) before each commit is a simple additional protection to put in place.