You have built a Model Context Protocol (MCP) server. It runs perfectly when integrated into the Claude Desktop app. However, when you attempt to run the MCP Inspector to debug a new tool or resource, you hit a wall. The connection hangs, times out, or immediately disconnects.
This is the "Transport Mismatch" problem, and it is the most common hurdle for developers adopting the MCP standard.
The issue is rarely your logic; it is almost always how the communication layer (Transport) is configured versus what the Inspector expects. This guide provides a deep technical analysis of why this breaks and details two distinct architectural patterns to fix it.
The Root Cause: Transport Layer Mismatch
To debug this effectively, we must understand the architecture of the Model Context Protocol. MCP relies on a client-host-server topology that is transport-agnostic. The SDK provides two primary transport mechanisms:
- StdioServerTransport: Communicates via Standard Input/Output (stdin/stdout). This is the default for local integrations (like Claude Desktop) because it allows the host application to spawn the server as a subprocess and manage its lifecycle directly.
- SSEServerTransport: Uses Server-Sent Events (SSE) for server-to-client updates and HTTP POST for client-to-server messages. This is required for remote servers or distributed systems.
Why The Inspector Fails
The MCP Inspector is a web-based application. Browsers cannot natively pipe data into a local process's standard input.
When you run a server configured with StdioServerTransport and try to connect the Inspector to localhost:3000, it fails because STDIO servers do not listen on TCP ports. They listen to the shell process that spawned them.
To debug an STDIO server, the Inspector must act as the parent process. To debug a networked server, you must implement the SSE transport layer.
Solution 1: Debugging STDIO Servers (The Proxy Method)
If your goal is to build a server for Claude Desktop, you likely want to keep using StdioServerTransport. You do not need to change your code to debug it; you need to change how you invoke the Inspector.
Instead of running your server separately, you must pass your server's execution command as an argument to the Inspector. The Inspector will spawn your Node process, attach to its STDIO streams, and bridge that to a WebSocket for the web UI.
The Correct Command
If your server is compiled to build/index.js, run this command in your terminal:
npx @modelcontextprotocol/inspector node build/index.js
Modern STDIO Implementation
Ensure your server entry point uses the modern initialization pattern. Below is a robust implementation using TypeScript and the latest SDK features.
// src/index.ts
import { Server } from "@modelcontextprotocol/sdk/server/index.js";
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
import {
CallToolRequestSchema,
ListToolsRequestSchema,
} from "@modelcontextprotocol/sdk/types.js";
// 1. Initialize the Server
const server = new Server(
{
name: "example-stdio-server",
version: "1.0.0",
},
{
capabilities: {
tools: {},
},
}
);
// 2. Define Tool Schemas
server.setRequestHandler(ListToolsRequestSchema, async () => {
return {
tools: [
{
name: "calculate_metric",
description: "Calculates a system metric based on input",
inputSchema: {
type: "object",
properties: {
value: { type: "number" },
},
required: ["value"],
},
},
],
};
});
// 3. Handle Tool Execution
server.setRequestHandler(CallToolRequestSchema, async (request) => {
if (request.params.name === "calculate_metric") {
const value = Number(request.params.arguments?.value || 0);
return {
content: [
{
type: "text",
text: `Processed metric: ${value * 1.5}`,
},
],
};
}
throw new Error("Tool not found");
});
// 4. Connect Transport
// Critical: This must be the last step.
async function main() {
const transport = new StdioServerTransport();
await server.connect(transport);
console.error("MCP Server running on STDIO"); // Use stderr for logs, stdout is for protocol!
}
main().catch((error) => {
console.error("Fatal error:", error);
process.exit(1);
});
Key Takeaway: Notice the logging uses console.error. If you use console.log, you will corrupt the JSON-RPC payload on stdout, causing the Inspector to crash with parse errors.
Solution 2: Debugging over HTTP (The SSE Method)
If you are building a standalone microservice or running inside Docker, you cannot rely on STDIO. You must implement SSEServerTransport.
This requires an HTTP server (like Express or Fastify) to handle the initial handshake and subsequent POST requests.
Valid SSE Implementation
This solution creates a dual-endpoint architecture:
- GET /sse: Establishes the long-lived connection for server-to-client pushes.
- POST /messages: Handles client-to-server JSON-RPC requests.
Prerequisites:
npm install express @modelcontextprotocol/sdk
npm install --save-dev @types/express
// src/server-http.ts
import express from "express";
import { Server } from "@modelcontextprotocol/sdk/server/index.js";
import { SSEServerTransport } from "@modelcontextprotocol/sdk/server/sse.js";
import {
CallToolRequestSchema,
ListToolsRequestSchema,
} from "@modelcontextprotocol/sdk/types.js";
const app = express();
const PORT = 3000;
// Initialize MCP Server
const server = new Server(
{
name: "example-http-server",
version: "1.0.0",
},
{
capabilities: {
tools: {},
},
}
);
// Register Tools (Same logic as STDIO)
server.setRequestHandler(ListToolsRequestSchema, async () => {
return {
tools: [{ name: "ping", description: "Health check", inputSchema: {} }],
};
});
server.setRequestHandler(CallToolRequestSchema, async (request) => {
return {
content: [{ type: "text", text: "pong" }],
};
});
// Transport Variable to track active connection
let transport: SSEServerTransport | null = null;
// Endpoint 1: SSE Handshake
app.get("/sse", async (req, res) => {
console.log("New SSE connection initiated");
transport = new SSEServerTransport("/messages", res);
await server.connect(transport);
// Clean up on close
req.on("close", () => {
console.log("SSE connection closed");
server.close();
});
});
// Endpoint 2: Client Messages (JSON-RPC)
app.post("/messages", async (req, res) => {
if (!transport) {
res.sendStatus(400);
return;
}
// Use the active transport to handle the incoming message
await transport.handlePostMessage(req, res);
});
app.listen(PORT, () => {
console.log(`MCP Server running on http://localhost:${PORT}/sse`);
});
connecting the Inspector
Once this server is running (node build/server-http.js), you do not use the npx proxy command. Instead:
- Open the MCP Inspector in your browser (or run
npx @modelcontextprotocol/inspector). - Select "Remote (SSE)" as the connection type.
- Enter the URL:
http://localhost:3000/sse.
Edge Cases and Common Pitfalls
Even with the correct code, environment issues can block connections.
1. Environment Variable Scoping
When using the "Solution 1" proxy method, the Inspector spawns a new shell. If you rely on .env files, they might not load automatically in that child process.
Fix: explicitly load environment variables in your run command:
# Loading env vars before the inspector command
export API_KEY=123 && npx @modelcontextprotocol/inspector node build/index.js
Or, use dotenv programmatically at the very top of your server code:
import "dotenv/config"; // Must be the first import
2. Zombie Processes (EADDRINUSE)
If you switch between STDIO and SSE frequently, Node processes often hang in the background, holding onto port 3000.
Fix: Before starting the inspector, force kill existing Node processes related to your project.
# Linux/Mac
lsof -i :3000 | xargs kill -9
3. Log Pollution
As mentioned in Solution 1, console.log writes to standard output. In MCP, standard output is reserved strictly for JSON-RPC messages. Any arbitrary string logged there (console.log("Starting...")) violates the protocol schema, causing the Inspector to disconnect immediately.
Fix: strictly use console.error() for debugging logs, or use a logging library (like Winston or Pino) configured to write to a file or stderr.
Conclusion
The MCP Inspector is a powerful tool, but it requires strict adherence to transport protocols. The rule of thumb is simple: if you want to inspect an existing script locally, use the command-line proxy argument. If you need to inspect a running service, build the SSE endpoint.
By isolating the transport layer from your tool logic, you can toggle between these modes—using StdioServerTransport for Claude Desktop deployment and SSEServerTransport for remote debugging and web integration.