MCP Best Practices

Decision reference for building production MCP servers with the TypeScript SDK. Not a tutorial - assumes you already have a working server and need to make it correct, fast, and secure.

Quick Reference

Component	Current	Next
Spec	2025-11-25 (spec.modelcontextprotocol.io)	-
TS SDK (stable)	v1.28.0 (@modelcontextprotocol/sdk)	v2 pre-alpha on main
TS SDK (v2)	Pre-alpha (@modelcontextprotocol/server, /client, /core)	Q1 2026 stable
JSON Schema	2020-12 default (explicit $schema supported)	-
Transport	Streamable HTTP (remote), stdio (local)	SSE removed in v2
Extensions	MCP Apps (GA), Auth Extensions (official)	Domain-specific WGs
Registry	Preview (registry)	GA pending

v1 imports (production today):

import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
import { WebStandardStreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/webStandardStreamableHttp.js";
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";

v2 imports (when stable):

import { McpServer } from "@modelcontextprotocol/server";
import { WebStandardStreamableHTTPServerTransport } from "@modelcontextprotocol/server";

Server Setup

Transport Decision

Scenario	Transport	Key Config
Remote, stateless (K8s, CF Workers)	WebStandardStreamableHTTPServerTransport	sessionIdGenerator: undefined, enableJsonResponse: true
Remote, stateful (long tasks, SSE)	WebStandardStreamableHTTPServerTransport	sessionIdGenerator: () => randomUUID()
Local CLI / Claude Desktop	StdioServerTransport	Default
Legacy SSE clients	SSE removed in v2 - migrate to Streamable HTTP	-

Stateless Pattern (recommended for remote deployment)

Per-request server+transport creation is the canonical pattern. Maintainer @ihrpr confirms: "each transport should have an instance of MCPServer" (#343). Sharing instances leaks cross-client data (GHSA-345p-7cg4-v4c7).

app.post("/mcp", async (c) => {
  const server = new McpServer({ name: "my-server", version: "1.0.0" });
  // Register tools, resources, prompts...
  registerTools(server);

  const transport = new WebStandardStreamableHTTPServerTransport({
    sessionIdGenerator: undefined,   // stateless - no session tracking
    enableJsonResponse: true,        // JSON responses, no SSE streaming
  });

  // All tools/resources must be registered before connect() (#893)
  try {
    await server.connect(transport);
    return transport.handleRequest(c.req.raw);
  } finally {
    await transport.close();
    await server.close();
  }
});

What to hoist to module level (don't recreate per request):

• Zod schemas (they never change)
• Annotation objects ({ readOnlyHint: true, ... })
• Tool description strings
• Payment configs, upstream API clients

The McpServer itself must be per-request, but its constant inputs should not be.

For deep dive on transports, sessions, HTTP/2 gotchas, and K8s deployment: see references/transport-patterns.md

Framework Integration

Hono (web-standard):

import { Hono } from "hono";
const app = new Hono();
app.post("/mcp", handleMcpRequest);  // WebStandardStreamableHTTPServerTransport
app.get("/mcp", handleMcpSse);       // Optional: SSE for server notifications
app.delete("/mcp", handleMcpDelete); // Optional: session termination

Cloudflare Workers: Same pattern - WebStandardStreamableHTTPServerTransport works natively in Workers runtime.

Express/Node (v2): Use @modelcontextprotocol/express middleware with NodeStreamableHTTPServerTransport (wraps the Web Standard transport for IncomingMessage/ServerResponse).

Tool Design

Registration API

v1 (current stable) - server.tool() works but has ambiguous overloads. Prefer the config-object form when possible:

server.tool("search_docs", "Search documents", {
  query: z.string().describe("Search query"),
  max_results: z.number().optional().describe("Max results (default 20)"),
}, { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
  async ({ query, max_results }) => { /* handler */ }
);

v2 (migration target) - registerTool() with config object:

server.registerTool("search_docs", {
  title: "Document Search",
  description: "Search documents by keyword or phrase",
  inputSchema: z.object({
    query: z.string().describe("Search query"),
    max_results: z.number().optional().describe("Max results (default 20)"),
  }),
  outputSchema: z.object({
    results: z.array(z.object({ id: z.string(), text: z.string() })),
    has_more: z.boolean(),
  }),
  annotations: { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
}, async ({ query, max_results }) => {
  const result = await fetchDocs(query, max_results);
  return {
    structuredContent: result,
    content: [{ type: "text", text: JSON.stringify(result) }],
  };
});

Naming

Spec (2025-11-25): 1-128 chars, case-sensitive. Allowed: A-Za-z0-9_-.

DO: search_docs, get_user_profile, admin.tools.list DON'T: search (too generic, collides across servers), Search Docs (spaces not allowed)

Service-prefix your tools (github_*, jira_*) when multiple servers are active - LLMs confuse generic names across servers.

Schema Rules

.describe() on every field - this is what LLMs use for argument generation.

For complete Zod-to-JSON-Schema conversion rules, what breaks silently, outputSchema/structuredContent patterns: see references/tool-schema-guide.md

Critical bugs:

• z.union() / z.discriminatedUnion() silently produce empty schemas (#1643). Use flat z.object() with z.enum() discriminator field instead.
• Plain JSON Schema objects silently dropped before v1.28.0. Fixed in v1.28 - now throws at registration (#1596).
• z.transform() stripped during conversion - JSON Schema can't represent transforms (#702).

Annotations

All are optional hints (untrusted from untrusted servers per spec):

Annotation	Default	Meaning
readOnlyHint	false	Tool doesn't modify its environment
destructiveHint	true	May perform destructive updates (only when readOnly=false)
idempotentHint	false	Repeated calls with same args have no additional effect
openWorldHint	true	Interacts with external entities (APIs, web)

Set them accurately - clients use them for consent prompts and auto-approval decisions.

Open SEPs expanding annotations:

• #1913 Trust and Sensitivity - data classification hints
• #1984 Comprehensive annotations for governance/UX
• #1561 unsafeOutputHint - output may contain untrusted content
• #1560 secretHint - tool handles secrets/credentials
• #1487 trustedHint - server attestation of tool trustworthiness

The "Lethal Trifecta": Combining (1) access to private data + (2) exposure to untrusted content + (3) external communication ability creates data theft conditions. Researchers demonstrated this with a malicious calendar event, an MCP calendar server, and a code execution tool. Design tool sets to avoid granting all three simultaneously.

Evaluation framework for new annotation proposals:

1. What client behavior changes? (No concrete action = don't add it)
2. Does it require trust to be useful? (If yes, doesn't help against untrusted servers)
3. Could _meta handle it? (Namespaced metadata better for single-deployment needs)
4. Does it help reason about tool combinations?
5. Is it a hint or contract? (Contracts belong in auth/transport/runtime layer)

Error Handling

Two distinct mechanisms with different LLM visibility:

Type	LLM Sees It?	Use For
Tool error (isError: true in CallToolResult)	Yes - enables self-correction	Input validation, API failures, business logic errors
Protocol error (JSON-RPC error response)	Maybe - clients MAY expose	Unknown tool, malformed request, server crash

Per SEP-1303 (merged into spec 2025-11-25): input validation errors MUST be tool execution errors, not protocol errors. The LLM needs to see "date must be in the future" to self-correct.

// DO: Tool execution error - LLM can self-correct
return {
  isError: true,
  content: [{ type: "text", text: "Date must be in the future. Current date: 2026-03-25" }],
};

// DON'T: Protocol error for validation - LLM can't see this
throw new McpError(ErrorCode.InvalidParams, "Invalid date");

Known bug: The SDK loses error.data when converting McpError to tool results (PR #1075). If you embed structured data in McpError's data field, it may not reach the client. Use isError: true tool results with structured content instead.

For full error taxonomy, code examples, and payment error patterns: see references/error-handling.md

Resources and Instructions

Server Instructions

Set in the initialization response - acts as a system-level hint to the LLM about how to use your server:

const server = new McpServer({
  name: "docs-api",
  version: "1.0.0",
  instructions: "Knowledge base API. Use search_docs for full-text search, get_doc for retrieval by ID. All tools are read-only.",
});

Resource Registration

Expose documentation or structured data via docs:// URI scheme:

server.resource("search-operators", "docs://search-operators", {
  title: "Search Operators Guide",
  description: "Supported search operators and syntax",
  mimeType: "text/markdown",
}, async () => ({
  contents: [{ uri: "docs://search-operators", text: operatorsMarkdown }],
}));

Performance

Module-Level Caching

The McpServer must be per-request, but everything else can be shared:

// Module-level (created once)
const SCHEMAS = {
  search: z.object({ query: z.string().describe("Search query") }),
  fetch: z.object({ id: z.string().describe("Resource ID") }),
};
const READ_ONLY_ANNOTATIONS = {
  readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true,
} as const;

// Per-request (created each time)
function createMcpServer(ctx: Context) {
  const server = new McpServer({ name: "my-server", version: "1.0.0" });
  server.tool("search", "Search", SCHEMAS.search, READ_ONLY_ANNOTATIONS, handler);
  return server;
}

Token Bloat Mitigation

Tool definitions consume context window before any conversation starts. GitHub MCP: 20,444 tokens for 80 tools (SEP-1576).

Strategies:

1. 5-15 tools per server - community sweet spot. Split beyond that.
2. Outcome-oriented tools - bundle multi-step operations into single tools (e.g., track_order(email) not get_user + list_orders + get_status).
3. Response granularity - return curated results, not raw API dumps. 800-token user object vs 20-token summary.
4. outputSchema + structuredContent - lets clients process data programmatically without LLM parsing overhead.
5. Dynamic tool loading - register only relevant tool subsets based on request context (e.g., ?tools=search,fetch query parameter).

No-Parameter Tools

For tools with no inputs, use explicit empty schema:

inputSchema: { type: "object" as const, additionalProperties: false }

Security

Top Threats (real-world incidents, 2025)

Attack	Example	Mitigation
Tool poisoning	Hidden instructions in descriptions (WhatsApp MCP, Apr 2025)	Review tool descriptions; clients should display them
Supply chain	Malicious npm packages (Smithery breach, Oct 2025)	Pin versions, audit dependencies
Command injection	child_process.exec with unsanitized input (CVE-2025-53967)	Never interpolate user input into shell commands
Cross-server shadowing	Malicious server overrides legitimate tool names	Service-prefix tool names; validate tool sources
Token theft	Over-privileged PATs with broad scopes	Minimal scopes; OAuth 2.1 Resource Indicators (RFC 8707)
Token passthrough	Server accepts/forwards tokens not issued for it	Validate audience claim; never transit client tokens to upstream APIs
SSRF	Malicious OAuth metadata URLs targeting internal services	HTTPS enforcement, block private IPs, validate redirect targets
Confused deputy	Proxy server consent cookies exploited via DCR	Per-client consent before forwarding to third-party auth
Session hijacking	Stolen/guessed session IDs for impersonation	Cryptographically random IDs, bind to user identity, never use for auth

Server-Side Requirements (spec normative)

• Validate all inputs at tool boundaries
• Implement access controls per user/session
• Rate limit tool invocations
• Sanitize outputs before returning to client
• Validate Origin header - respond 403 for invalid origins (2025-11-25 requirement)
• Require MCP-Protocol-Version header on all requests after initialization (spec 2025-06-18+)
• Bind local servers to localhost (127.0.0.1) only

Auth (OAuth 2.1)

MCP normatively requires OAuth 2.1 (draft-ietf-oauth-v2-1-13). The spec states: "Authorization servers MUST implement OAuth 2.1." PKCE is mandatory, implicit flow is removed. Always build against OAuth 2.1 - not 2.0.

MCP servers are OAuth 2.1 Resource Servers. Clients MUST include Resource Indicators (RFC 8707) binding tokens to specific servers. Key requirements:

• Validate audience - reject tokens not issued for your server (token passthrough is explicitly forbidden)
• PKCE mandatory - use S256 code challenge method
• Short-lived tokens - reduce blast radius of leaked credentials
• Scope minimization - start with minimal scopes, elevate incrementally via WWW-Authenticate challenges
• Don't implement token validation yourself - use tested libraries (Keycloak, Auth0, etc.)
• Don't log credentials - never log Authorization headers, tokens, or secrets

For full security attack/mitigation patterns and auth implementation details: see references/security-auth.md

Known SDK Bugs

Issue	Severity	Status	Workaround
#1643 - z.union()/z.discriminatedUnion() silently dropped	High	Open	Use flat z.object() + z.enum()
#1699 - Transport closure stack overflow (15-25+ concurrent)	High	Open	uncaughtException handler + process restart
#1619 - HTTP/2 + SSE Content-Length error	Medium	Open	Use enableJsonResponse: true or avoid HTTP/2 upstream
#893 - Dynamic registration after connect blocked	Medium	Open	Register all tools/resources before connect()
#1596 - Plain JSON Schema silently dropped	Fixed	v1.28.0	Upgrade to v1.28+
GHSA-345p-7cg4-v4c7 - Shared instances leak cross-client data	Critical	v1.26.0	Per-request server+transport (the canonical pattern)

V2 Migration

For comprehensive migration guide with all breaking changes and before/after code: see references/v2-migration.md

Key breaking changes:

1. Package split: @modelcontextprotocol/sdk -> @modelcontextprotocol/server + /client + /core
2. ESM only, Node.js 20+
3. Zod v4 required (or any Standard Schema library)
4. McpError -> ProtocolError (from @modelcontextprotocol/core)
5. extra parameter -> structured ctx with ctx.mcpReq
6. server.tool() -> registerTool() (config object, not positional args)
7. SSE server transport removed (clients can still connect to legacy SSE servers)
8. @modelcontextprotocol/hono and @modelcontextprotocol/express middleware packages
9. DNS rebinding protection enabled by default for localhost servers

v1.x gets 6 more months of support after v2 stable ships. No rush, but write new code with v2 patterns in mind.

Extensions

MCP extensions are optional, strictly additive capabilities on top of the core protocol. Both sides negotiate support during initialization via extensions in capabilities.

Identifiers: {vendor-prefix}/{extension-name}. Official: io.modelcontextprotocol/*. Third-party: reversed domain (e.g., com.example/my-ext).

Official Extensions

Extension	Identifier	Purpose
MCP Apps	io.modelcontextprotocol/ui	Interactive HTML UIs in chat (charts, forms, dashboards)
OAuth Client Credentials	io.modelcontextprotocol/oauth-client-credentials	Machine-to-machine auth (CI/CD, daemons, server-to-server)
Enterprise-Managed Auth	io.modelcontextprotocol/enterprise-managed-authorization	Centralized access control via enterprise IdP

Client support: Claude (web + Desktop), ChatGPT, VS Code Copilot, Goose, Postman, MCPJam all support MCP Apps. Auth extensions not yet widely adopted.

For MCP Apps architecture, ext-apps SDK, and build patterns: see references/mcp-apps.md For extensions system, auth extensions, and MCP Registry: see references/extensions-registry.md

Server Capabilities Beyond Tools

Capability	Purpose	v2 API
Elicitation	Request structured user input mid-tool	ctx.mcpReq.elicitInput()
Sampling	Request LLM completion from client	ctx.mcpReq.requestSampling()
Tasks (SEP-1686)	Long-running ops with lifecycle management	Pending
Progress	Incremental progress on requests	ctx.mcpReq.sendProgress()