[Self-hosted] MCP native mode not initializing — “bad request: server not initialized”

[Thiago_Pinheiro]

Hi all, I’m running a production self-hosted n8n instance (v1.21.0, Docker Compose) and trying to enable MCP (Modular Control Plane) in native mode with one main and one runner container.

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What I’ve already set up:

• Docker Compose with:

yaml

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services:
  n8n-main:
    image: n8nio/n8n:latest
    environment:
      - N8N_MCP_SERVER=true
      - EXECUTIONS_MODE=queue
      - N8N_RUNNER_MODE=main
      - N8N_MCP_SKIP_SSL_VALIDATION=true
      - N8N_MCP_USE_REVERSE_PROXY=true
      - N8N_MCP_TRUST_PROXY=true

  n8n-runner:
    image: n8nio/n8n:latest
    environment:
      - EXECUTIONS_MODE=queue
      - N8N_RUNNER_MODE=runner
      - N8N_MCP_SKIP_SSL_VALIDATION=true
      - N8N_MCP_USE_REVERSE_PROXY=true
      - N8N_MCP_TRUST_PROXY=true

• Reverse proxy using NGINX (with HTTPS) and a specific block for /mcp/, including SSE proxy settings:

nginx

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location /mcp/ {
    proxy_pass http://n8n-main:5678;
    proxy_http_version 1.1;
    proxy_buffering off;
    proxy_cache off;
    proxy_read_timeout 3600s;
    proxy_send_timeout 3600s;
    gzip off;
    chunked_transfer_encoding off;

    proxy_set_header Host $host;
    proxy_set_header X-Real-IP $remote_addr;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Forwarded-Proto $scheme;
    proxy_set_header Connection '';
}

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The issue:

Even after all of this, accessing the /mcp/.../sse endpoint returns:

json

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{
  "jsonrpc": "2.0",
  "error": {
    "code": -32000,
    "message": "bad request: server not initialized"
  },
  "id": null
}

• Both n8n-main and n8n-runner containers are up
• UI works fine
• No workflows execute, and no runner appears to register with MCP
• Logs do not show any “registered” or “initialized” messages

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What I’m trying to understand:

• Is there something missing in the init handshake from the runner to MCP?
• Are there other required settings not documented for this setup?
• Could this be related to the reverse proxy or Docker network setup?
• How can I validate that MCP is waiting for runners?

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Any ideas, examples or guidance would be greatly appreciated. Thanks in advance!

[Vinodraj_Jayaraman]

I’m facing the same. Any one have answer ?