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) | Unreleased draft: stateless/sessionless overhaul (see "Spec Draft Direction") | | TS SDK (stable) | v1.29.0 (@modelcontextprotocol/sdk) | v2 alpha published | | TS SDK (v2) | Alpha (2.0.0-alpha.2 on npm, Apr 2026): /server, /client, /core, /hono, /express, /node, /fastify | Stable pending; only alpha published | | JSON Schema | 2020-12 default (explicit $schema supported) | - | | Transport | Streamable HTTP (remote), stdio (local) | SSE + WebSocket removed in v2 | | Extensions | MCP Apps (Stable, SEP-1865), Auth Extensions (official) | Domain-specific WGs | | Registry | Preview with v0.1 API freeze since 2025-10-24 (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(name, description, zodShape, annotations, handler). Positional overloads are ambiguous; same fields as v2 below minus outputSchema.

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 {
    // Both channels carry IDENTICAL bytes. Divergent payloads = the text block
    // silently vanishes on Claude Code/Codex/Copilot. See "Tool Result Delivery" below.
    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 (detail + status in the Known SDK Bugs table below; conversion deep-dive in the reference):

• z.union()/z.discriminatedUnion() silently produce empty schemas on all released v1 (#1643) - use flat z.object() + z.enum() discriminator.
• Raw JSON Schema objects throw at registration since v1.28 (#1596); z.transform() is silently stripped (#702).
• Client AJV rejects unstripped structuredContent extras (Zod v4 emits additionalProperties: false): .parse() upstream data before assigning, or .passthrough() for intentional extras.

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.

The "Lethal Trifecta": combining (1) access to private data + (2) exposure to untrusted content + (3) external communication ability creates data-theft conditions (demonstrated via a malicious calendar event + MCP calendar server + code-execution tool). Design tool sets so no single agent holds all three.

Tool Result Delivery: content vs structuredContent

The footgun: when a tool returns BOTH a text content block and structuredContent, several major clients (Claude Code, Codex CLI, VS Code Copilot, Goose) silently drop the text block and forward only structuredContent to the model. If the two payloads differ, the human-readable one vanishes. This is client behavior the spec does not constrain - not an SDK transform. Don't return both channels expecting both to reach the model.

Empirically tested - Claude Code 2.1.165 (MCP 2025-11-25)

Measured with claude -p --output-format=stream-json, reading the exact tool_result the model received:

| Tool returns | What the model receives | |--------------|-------------------------| | One text block, no structuredContent | text verbatim | | content: [] + structuredContent | JSON.stringify(structuredContent) as a string in the content slot - works | | text block + structuredContent | text block silently dropped; structuredContent wins | | text + structuredContent + outputSchema | same - outputSchema makes zero difference | | two text blocks, no structuredContent | both preserved verbatim |

structuredContent is not a separate typed channel to the model on Claude Code - it is stringified into the standard tool_result content slot, so it costs the same tokens as the equivalent JSON-as-text. It does not buy cheaper or out-of-band structured data.

Intentional, per Anthropic maintainer (anthropics/claude-code#9962): structuredContent support landed in Claude Code v2.0.21 and "we made structuredContent the default when both formats are present... optimizing for agent performance." Reproduced across unrelated servers (Laravel, Roblox Studio, YouTube) - host-side precedence, not a server bug.

What the spec actually says (2025-11-25)

• content is required on CallToolResult (content: ContentBlock[]); structuredContent? and isError? are optional. An empty content: [] is schema-valid.
• Backwards-compat SHOULD (the only relevant normative line): "a tool that returns structured content SHOULD also return the serialized JSON in a TextContent block."
• No precedence rule. The spec never says which field a client should prefer when both are present (Discussion #1563; clarification in flight via SEP-1624 -> SEP-2200). That gap is the documented root cause of client divergence.
• outputSchema: servers MUST produce conforming structuredContent; clients SHOULD (not MUST) validate it.

The official TypeScript SDK passes both fields through verbatim on server and client (the only mutation is optional outputSchema validation, which can throw). Any stringify-into-content you observe is the host harness, not the SDK.

Cross-client behavior (the matrix above is Claude Code only)

| Client | When both content + structuredContent present | |--------|---------------------------------------------------| | Claude Code CLI, OpenAI Codex CLI, VS Code Copilot, Goose | shadow - only structuredContent reaches the model (text dropped) | | Cursor, Claude.ai web, ChatGPT MCP connector | prefer content / surface both to the model | | Google ADK (framework) | forwards both by default; content-only is opt-in |

VS Code maintainer's framing (microsoft/vscode#290063): "structuredContent actually should not be presented to the model, its use case is PTC [programmatic tool calling]." Clients disagree on enforcing that, so portable servers can't rely on it either way. (Non-Claude-Code rows come from issue trackers/maintainer statements, not the stream-json harness - treat exact delivery as client-version-dependent.)

The rule for server authors

• DON'T return divergent content and structuredContent (e.g. a rendered ASCII table as text + different JSON as structured). On shadowing clients the text silently disappears and only the JSON reaches the model.
• DO, if you emit structuredContent, mirror the same bytes into a text block: content: [{ type: "text", text: JSON.stringify(payload) }]. This is the spec's backwards-compat SHOULD. Shadowing clients use the structured copy; others fall back to the identical text - either way the model gets the data. Mirroring does not double tokens on shadowing clients (they drop the text).
• PREFER one channel per tool / per mode. For a human-readable rendering (table, summary) to reach the model, return it as text only, no structuredContent - or expose a format: "table" | "json" arg (table -> text-only; json -> JSON mirrored into both channels). Both are empirically valid on Claude Code and keep one channel per call.
• outputSchema gates client-side validation only; it does not make the text block survive on shadowing clients.

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 SDK behavior: When the SDK converts an McpError thrown from a tool handler into a CallToolResult, the error.data field is dropped. If you embed structured data in McpError's data field, it may not reach the client. The x402/MPP MCP ecosystem standardized on isError: true tool results with structuredContent for this reason. (One exception: code -32042 "Payment Required" survives McpServer end-to-end with error.data intact - see references/error-handling.md.)

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 - typed output for programmatic/PTC clients. Caveat: on shadowing clients (Claude Code et al.) structuredContent is stringified into the model's context at the same token cost as text - it is not a free out-of-band channel. See "Tool Result Delivery: content vs structuredContent".
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, 2025-2026)

| 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 | | Stdio config injection | User-controlled input reaches StdioServerParameters without sanitization (OX Security disclosure, 2026-04-15) | Sanitize stdio config inputs in client code; prefer first-party servers; treat by Anthropic as "by design" - not patched in SDK | | 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 | | Cross-client response leak | Shared McpServer/transport reused across clients (CVE-2026-25536, affects v1.10.0-1.25.3) | Require SDK ≥ v1.26.0; per-request server+transport | | UriTemplate ReDoS | Malicious URI patterns (CVE-2026-0621) | Upgrade to v1.25.2+ / v2.0.0-alpha.1+ |

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; "Authorization servers MUST implement OAuth 2.1"), not 2.0 - PKCE mandatory, implicit flow removed. Servers are OAuth 2.1 Resource Servers; clients MUST send Resource Indicators (RFC 8707) binding tokens to your server.

• Validate audience - reject tokens not issued for your server (passthrough is forbidden)
• PKCE S256, short-lived tokens, minimal scopes (elevate via WWW-Authenticate challenges)
• Use a tested validation library (Keycloak, Auth0, ...) - don't roll your own; never log Authorization headers/tokens/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 | Fixed in v2 line (PR #1796); v1.x backport PR #2017 still open | Use flat z.object() + z.enum() - bug present on all released v1 | | #1699 - Transport closure stack overflow (15-25+ concurrent) | High | Fixed in PR #1788 (closed 2026-04-02) | Upgrade to ≥ v1.29.0 / v2 alpha | | #1619 - HTTP/2 + SSE Content-Length error | Medium | Closed (reclassified to upstream @hono/node-server#266) | 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+ | | Client AJV strict rejects unstripped structuredContent extras | High | Behavior, not bug | Server .parse() upstream data before returning, or use .passthrough() | | GHSA-345p-7cg4-v4c7 / CVE-2026-25536 - Shared instances leak cross-client data | Critical | Fixed v1.26.0 | Require ≥ v1.26.0 (or v2.0.0-alpha.1+); per-request server+transport | | CVE-2026-0621 - UriTemplate ReDoS | Medium | Fixed v1.25.2 / v2.0.0-alpha.1 | Upgrade |

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.

Spec Draft Direction (post-2025-11-25, unreleased)

2025-11-25 is the latest released revision (everything above targets it). The next spec is still an unversioned draft - not implementable in any released SDK - but it sets a clear direction worth knowing before you commit design decisions today. The TS SDK has begun landing the wire-contract types on main against a 2026-07-28 target (#2252, 2026-06-08).

Decision-relevant shifts:

• MCP becomes stateless and sessionless. The draft removes the initialize/notifications/initialized handshake and the Mcp-Session-Id header entirely (SEP-2575, SEP-2567). Every request carries its protocol version, client identity, and capabilities in _meta. Servers needing cross-call state return a server-minted handle from a creation tool and accept it as an ordinary tool argument - not protocol sessions. This validates the skill's existing "prefer stateless" stance; do not build new servers on session affinity.
• server/discover RPC replaces initialize-time negotiation for advertising versions/capabilities/identity (SEP-2575).
• Multi Round-Trip Requests (MRTR) replace server-initiated requests (roots/list, sampling/createMessage, elicitation/create): a tool returns inputRequests; the client answers with inputResponses on the next call (SEP-2322).
• Formal feature lifecycle (Active/Deprecated/Removed, 12-month minimum window, deprecated registry, SEP-2596). Under it, Roots, Sampling, and Logging are now formally Deprecated (SEP-2577, the advisory deprecation above made formal) and the HTTP+SSE transport is reclassified Deprecated (SEP-2596).
• Auth: OAuth 2.0 Dynamic Client Registration is deprecated in favor of Client ID Metadata Documents (CIMD) (PR #2858); clients MUST validate a present iss (RFC 9207, SEP-2468) and key persisted credentials by issuer (SEP-2352).
• Caching: list/read results gain required ttlMs + cacheScope (public/private) via a CacheableResult interface (SEP-2549); tools SHOULD be returned in deterministic order for prompt-cache hits.
• HTTP: Streamable HTTP POSTs require Mcp-Method/Mcp-Name headers, with optional x-mcp-header to mirror tool params into headers (SEP-2243).
• Schemas loosen: inputSchema/outputSchema accept any JSON Schema 2020-12 keywords (with $ref resolution), and structuredContent may be any JSON value (SEP-2106).

The content vs structuredContent dual-delivery footgun is unchanged in the draft - the backwards-compat SHOULD persists and no precedence rule landed, so the guidance above still holds.

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 | Long-running ops with lifecycle management | Official extension (SEP-2663) | | Progress | Incremental progress on requests | ctx.mcpReq.sendProgress() |

Deprecation / status notice: SEP-2577 (final, 2026-05-15) advisory-deprecates Roots, Sampling, and Logging - no wire changes, features stay functional for 1+ year, but design new servers without them. Tasks moved out of the core 2025-11-25 spec (the experimental tasks feature there is removed) into an official extension (SEP-2663, final, 2026-05-15): a server may answer tools/call with an async task handle the client polls via tasks/get, tasks/update, tasks/cancel.