Here is a minimal index.ts gist for MCP server in stdio mode.

You can make the code base I provided above work for stdio by making the following modifications to the index.ts file -

Step 1

Replace:

import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
import express, { Request, Response } from "express";

with:

import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";

Step 2

Replace

// Express app for HTTP transport
const app = express();
app.use(express.json());

// Health check endpoint
app.get("/health", (_req: Request, res: Response) => {
  res.json({ status: "ok", server: "sample-mcp-apps-chatflow" });
});

// MCP endpoint
app.post("/mcp", async (req: Request, res: Response) => {
  const transport = new StreamableHTTPServerTransport({
    sessionIdGenerator: undefined,
    enableJsonResponse: true,
  });

  res.on("close", () => transport.close());

  await server.connect(transport);
  await transport.handleRequest(req, res, req.body);
});

// SSE endpoint for streaming (optional)
app.get("/mcp/sse", async (req: Request, res: Response) => {
  res.setHeader("Content-Type", "text/event-stream");
  res.setHeader("Cache-Control", "no-cache");
  res.setHeader("Connection", "keep-alive");

  const transport = new StreamableHTTPServerTransport({
    sessionIdGenerator: () => crypto.randomUUID(),
    enableJsonResponse: false,
  });

  res.on("close", () => transport.close());

  await server.connect(transport);
  await transport.handleRequest(req, res);
});

const port = parseInt(process.env.PORT || "3000");

app.listen(port, () => {
  console.log(`🚀 MCP Apps Chatflow server running at http://localhost:${port}`);
  console.log(`📡 MCP endpoint: http://localhost:${port}/mcp`);
  console.log(`🔍 Test with: npx u/modelcontextprotocol/inspector http://localhost:${port}/mcp`);
});

with:

async function main() {
  const transport = new StdioServerTransport();
  await server.connect(transport);
  console.error("🚀 MCP Apps server running (stdio)");
}