Best practices for securing your MCP server — API keys, validation, rate limiting, and more.

Security

MCP servers handle privileged operations — database queries, file access, API calls — so security should be a first-class concern.

Environment Variables

Never hardcode secrets. Use environment variables for API keys, tokens, and database credentials.

import { createServer, tool } from "mcpcraft-sdk"

const server = createServer({ name: "secure-server" })

server.add(tool({
  name: "query_database",
  input: {
    query: { type: "string", description: "SQL query" }
  },
  run: async ({ query }) => {
    const db = await connect(process.env.DATABASE_URL!)
    return db.query(query)
  }
}))

# .env
DATABASE_URL=postgres://user:pass@host:5432/db
API_KEY=sk-proj-...

Input Validation

MCPCraft auto-generates Zod validators from your input definitions, but you should add additional guardrails for sensitive operations.

server.add(tool({
  name: "send_email",
  input: {
    to: { type: "string", description: "Recipient email" },
    body: { type: "string", description: "Email body" }
  },
  run: async ({ to, body }) => {
    // Additional validation beyond type checking
    if (!to.includes("@")) {
      throw new Error("Invalid email address")
    }
    if (body.length > 10000) {
      throw new Error("Email body too long")
    }
    return sendMail(to, body)
  }
}))

Rate Limiting

When exposing your server over SSE, protect against abuse with rate limiting.

const rateLimits = new Map<string, number>()
const RATE_LIMIT = 100 // requests per minute

server.add(tool({
  name: "expensive_operation",
  input: {
    data: { type: "string", description: "Input data" }
  },
  run: async ({ data }, context) => {
    const clientId = context.clientId ?? "unknown"
    const now = Date.now()
    const last = rateLimits.get(clientId) ?? 0

    if (now - last < 60000 / RATE_LIMIT) {
      throw new Error("Rate limit exceeded")
    }
    rateLimits.set(clientId, now)

    return process(data)
  }
}))

API Key Authentication

For SSE-based servers, require authentication on every request.

import { createServer } from "mcpcraft-sdk"

const server = createServer({
  name: "auth-server",
  authenticate: async (headers) => {
    const key = headers["x-api-key"]
    if (!key || key !== process.env.API_KEY) {
      throw new Error("Unauthorized")
    }
  }
})

MCP Security Best Practices

Practice	Recommendation
Least privilege	Give each tool only the access it needs
Allow lists	Restrict file system access to specific directories
Read-only by default	Make mutating tools opt-in
Audit logging	Log all tool invocations with timestamps and client IDs
Timeouts	Set per-tool execution time limits
Error messages	Don't leak internal details in error responses

Example: Secure File Server

const ALLOWED_DIR = process.env.ALLOWED_DIR ?? "./data"

server.add(tool({
  name: "read_file",
  description: "Read a file from the allowed directory",
  input: {
    path: { type: "string", description: "Relative file path" }
  },
  run: async ({ path }) => {
    // Prevent directory traversal
    const resolved = path.resolve(ALLOWED_DIR, path)
    if (!resolved.startsWith(path.resolve(ALLOWED_DIR))) {
      throw new Error("Access denied")
    }
    return readFile(resolved, "utf-8")
  }
}))

Next Steps

Authentication — API key and OAuth patterns
Deployment — Production deployment guides
Testing — Test your server security

Security

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