Obsidian MCP Server — Setup, Daily Use & Cloud Migration

Architecture

YOUR WINDOWS MACHINE (local, free)
├── Obsidian App (vault + Local REST API plugin on port 27124)
├── obsidian-mcp-server (HTTP on port 3010, translates MCP ↔ REST)
├── Docker
│   └── n8n container (connects to MCP via host.docker.internal:3010)
└── Cloudflare Tunnel (exposes n8n UI only, NOT the MCP server)

Security: Port 3010 is only accessible from your machine + Docker containers. Windows Firewall blocks all external access. Cloudflare tunnel only routes n8n (port 5678). The MCP server is invisible to the internet.

One-Time Setup

1. Install prerequisites (already done if Claude Code works)

# Verify Node.js and npx are available
node -v
npx -v

2. Create the .env config file

cd "a:\_Coding_Notes_Projects_IMP_\MAJOR PROJECTS\AmanSuryavanshi.dev\Omni-Post-AI-Automation"
copy .env.obsidian-mcp.example .env.obsidian-mcp

Edit .env.obsidian-mcp and paste your Obsidian API key:

• Open Obsidian > Settings > Community Plugins > Local REST API > copy the API Key
• Replace PASTE_YOUR_OBSIDIAN_API_KEY_HERE with your actual key

3. Ensure Docker can reach the host

Check your docker-compose.yml has:

services:
  n8n:
    # ... your existing config ...
    extra_hosts:
      - "host.docker.internal:host-gateway"

Docker Desktop on Windows usually has this by default, but add it explicitly.

4. Configure n8n MCP Client Tool node

In n8n, on the MCP Client Tool node attached to your Obsidian AI Agent:

5. First test

1. Open Obsidian
2. Double-click start-obsidian-mcp.bat
3. Wait for: StreamableHttp endpoint: http://localhost:3010/mcp
4. Optional health check (same terminal or another shell):

curl http://localhost:3010/healthz

Expected response: ok 4. In n8n, open the MCP Client Tool node — tools should now list in the dropdown 5. Run the Obsidian AI Agent node — it should fetch vault context

Daily Commands (3 terminals)

Every time you start your workflow:

Terminal 1: Start Obsidian MCP Server (recommended: watchdog)

# First: open Obsidian manually (needs to be running)
# Then start watchdog for auto-recovery:
powershell -NoProfile -ExecutionPolicy Bypass -File "A:\.n8n\n8n-local-docker\scripts\watch-obsidian-mcp.ps1"

Watchdog will health-check /healthz and auto-restart bridge on repeated failures.

Alternative (manual, no watchdog):

cd "a:\_Coding_Notes_Projects_IMP_\MAJOR PROJECTS\AmanSuryavanshi.dev\Omni-Post-AI-Automation"
.\start-obsidian-mcp.bat

Terminal 2: Start n8n Docker

# Your existing n8n Docker command
docker compose up -d
# or: docker start <your-n8n-container-name>

Terminal 3: Start Cloudflare Tunnel

# Your existing Cloudflare tunnel command
cloudflared tunnel run <your-tunnel-name>

Order matters:

1. Obsidian must be open FIRST (REST API needs the app)
2. MCP server starts SECOND (needs Obsidian REST API)
3. n8n starts THIRD (needs MCP server to list tools)
4. Cloudflare tunnel can start anytime (only routes n8n UI)

Shutdown:

• Ctrl+C in Terminal 1 (stops MCP server)
• docker compose down in Terminal 2 (stops n8n)
• Ctrl+C in Terminal 3 (stops tunnel)
• Close Obsidian whenever

Security Model

Local (current setup) — already secure

Nobody on the internet can reach your MCP server. It's local-only.

Cloud (when you migrate) — add JWT auth

When moving to cloud, uncomment these in .env.obsidian-mcp:

MCP_AUTH_MODE=jwt
MCP_AUTH_SECRET_KEY=<your-32-char-random-string>

Then in n8n:

• MCP Client Tool > Authentication > Bearer Auth
• Create credential with the JWT token

Cloud Migration Guide

When you'd move to cloud

• You want 24/7 uptime (workflows run while your PC is off)
• You want to trigger workflows from webhooks without your PC being on

The hard constraint

Obsidian MCP server needs the Obsidian desktop app running (for the Local REST API). This means cloud deployment requires either:

Option A: Keep MCP local, move only n8n to cloud (recommended, free)

CLOUD (VPS / Oracle Free Tier)
├── n8n (Docker)
└── Cloudflare Tunnel (exposes n8n)

YOUR PC (local)
├── Obsidian (must be open)
├── obsidian-mcp-server (HTTP mode)
└── Tailscale (private VPN, free tier)
     └── n8n connects to MCP via Tailscale IP

Why this works:

• Oracle Cloud Free Tier: 4 ARM CPUs, 24GB RAM, always free
• Tailscale: free for personal use (up to 100 devices)
• Your MCP server stays on your PC, only accessible via Tailscale private network
• n8n on cloud calls http://<your-tailscale-ip>:3010/mcp

Limitation: Your PC must be on for the Obsidian overlay to work.

• If your PC is off, the overlay fails gracefully and n8n uses Portfolio API only.

Setup steps:

1. Get Oracle Cloud Free Tier account
2. Create an ARM instance (Ampere A1, 4 OCPUs, 24GB RAM)
3. Install Docker + n8n on the instance
4. Install Tailscale on both your PC and the cloud instance
5. Update n8n MCP Client Tool endpoint to: http://<pc-tailscale-ip>:3010/mcp
6. Enable JWT auth on MCP server (since traffic crosses the network now)
7. Set up Cloudflare tunnel on the cloud instance for n8n UI

Option B: Full cloud with vault sync (advanced, free)

CLOUD (VPS)
├── n8n (Docker)
├── obsidian-mcp-server (Docker sidecar)
├── Obsidian vault files (synced via Git)
└── File-based vault reader (no Obsidian app needed)

Approach: Instead of depending on the Obsidian desktop app, sync your vault files to the cloud via Git:

1. Push vault to a private GitHub repo (or use Obsidian Git plugin)
2. Clone the vault on the cloud instance
3. Use a file-based MCP server that reads markdown directly (e.g., stevenstavrakis/obsidian-mcp which can work with raw files)
4. Set up a cron job to git pull every 10 minutes

Tradeoff: You lose real-time vault access (10-min delay) but gain full independence from your PC.

Option C: Hybrid — Portfolio API for cloud, Obsidian overlay when local

This is what we already built. The workflow runs fine with just Portfolio API. When your PC is on and MCP server is running, the overlay adds fresh vault context. When your PC is off, the overlay silently falls back.

This is the recommended default. Zero cloud cost. Zero risk. Full quality when local.

Free Tier Reference

Troubleshooting

MCP server won't start

• Is Obsidian open? The Local REST API plugin needs the app running.
• Is the API key correct in .env.obsidian-mcp?
• Is port 3010 already in use? Check: netstat -ano | findstr :3010

n8n can't connect to MCP server

• Is the MCP server running? Check Terminal 1 for the StreamableHttp endpoint line.
• Is Docker Desktop running? host.docker.internal needs Docker Desktop.
• Check health endpoint from host: curl http://localhost:3010/healthz (must return ok).
• Try from inside Docker:
  • docker exec -it <n8n-container> curl http://host.docker.internal:3010/healthz
  • docker exec -it <n8n-container> curl http://host.docker.internal:3010/mcp
• If you see intermittent timeout (MCP error -32001):
  1. If watchdog is running, wait one cycle (~20-60s) for auto-restart.
  2. If no recovery, restart Obsidian app.
  3. Restart watchdog or rerun start-obsidian-mcp.ps1.

Tools not listing in n8n dropdown

• Connection must work first (see above)
• Try switching Tools to Include to "All", save, then switch back to "Selected"
• Close and reopen the MCP Client Tool node

Obsidian overlay skipped in workflow output

• Check _meta.obsidianOverlay in the Personal Context Builder output
• If it says skipped: MCP server was unreachable or returned empty data
• This is safe — workflow continues with Portfolio API only