Feature Request: Support for Multiple Obsidian Vaults

[fobert789]

Summary

I would like to request support for connecting to multiple Obsidian vaults simultaneously, or at least an easier way to switch between different vaults without reconfiguring the MCP server.

Current Situation

Currently, the MCP server connects to a single Obsidian instance via the Local REST API plugin using one API key, host, and port. This means users can only access one vault at a time and need to:

1. Switch vaults manually in Obsidian
2. Or reconfigure the MCP server settings
3. Or run multiple Obsidian instances on different ports

Use Case

I have multiple Obsidian vaults for different purposes:

• A main work/knowledge vault
• A personal projects vault
• Potentially other specialized vaults

Being able to access multiple vaults would greatly improve workflow efficiency, especially when working with AI assistants that could help organize and cross-reference information across different knowledge domains.

Possible Solutions

I see a few potential approaches:

1. Multiple vault configuration: Allow specifying multiple vault configurations in the MCP settings, perhaps with vault identifiers
2. Vault switching command: Add a tool/command to switch between pre-configured vaults
3. Multi-instance support: Better documentation on running multiple Obsidian instances with different ports

Related Work

I noticed that StevenStavrakis/obsidian-mcp seems to support multiple vault paths in their configuration:

{
  "command": "node",
  "args": ["<path>/build/main.js", "/path/to/vault1", "/path/to/vault2"]
}

Additional Context

This is my first issue on GitHub, so please let me know if I should provide any additional information or if there's a better way to structure this request.

Configuration example I'm currently using:

\"mcp-obsidian\": {
  \"command\": \"uvx\",
  \"args\": [\"mcp-obsidian\"],
  \"env\": {
    \"OBSIDIAN_API_KEY\": \"...\",
    \"OBSIDIAN_HOST\": \"127.0.0.1\",
    \"OBSIDIAN_PORT\": \"27124\"
  }
}

Thank you for this great MCP server! 🙏

[stefanspycher]

Kudos to @fobert789 for this comprehensive report, and +1 to the request.
I have the exact same use case, and running into issues with Claude Desktop.
it seems regardless of the port settings of the second vault Local Rest API configuration, Claude is using the port settings from the first (and working) configuration.

my current claude_desktop_config.json looks as follows

"mcp-obsidian-v2": { "command": "uvx", "args": ["mcp-obsidian"], "env": { "OBSIDIAN_API_KEY": "API Key 1", "OBSIDIAN_HOST": "127.0.0.1", "OBSIDIAN_PORT": "27124" } }, "mcp-obsidian-MemPal": { "command": "uvx", "args": ["mcp-obsidian"], "env": { "OBSIDIAN_API_KEY": "API Key 2", "OBSIDIAN_HOST": "localhost", "OBSIDIAN_PORT": "38318" } },

with this error in the log file for the 2nd mcp server:

ERROR:mcp-obsidian:Request failed: HTTPSConnectionPool(host='127.0.0.1', port=27124): Max retries exceeded with url: /vault/ (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x10c517e00>: Failed to establish a new connection: [Errno 61] Connection refused'))

[vlcinsky]

Claude Desktop with Multiple Obsidian Vaults

This guide explains how to configure Claude Desktop to work with multiple Obsidian vaults simultaneously using the Model Context Protocol (MCP). The setup allows Claude to read from and edit content in multiple vaults at once.

Prerequisites

Before starting, ensure you have:

• Claude Desktop installed and running
• Multiple Obsidian vaults set up
• Local REST API Obsidian Plugin installed in each vault you want to connect
• MCP Obsidian server cloned from https://github.com/MarkusPfundstein/mcp-obsidian - clone this repository to a local directory and use that path in your configuration
• Basic familiarity with JSON configuration files

Overview

My original configuration for Claude Desktop to work with Obsidian was based on the YouTube video (12min24s) [Let Claude Automate Your Obsidian Notes: Second Brain AI Agent (MCP)](https://www.youtube.com/watch?v=VeTnndXyJQI). Later, I needed to enable access to multiple vaults simultaneously.

Successfully connecting Claude Desktop to multiple Obsidian vaults requires:

1. Enabling Local REST API plugins independently in each vault
2. Using different ports for each vault to prevent conflicts
3. Configuring separate MCP server entries in Claude Desktop's configuration
4. Setting environment variables for each vault connection

Key Concepts

MCP Server Configuration Names

Names of MCP client configurations in Claude Desktop are arbitrary - you don't need to use mcp-obsidian. Descriptive names like obsidian-work-vault or obsidian-personal work better for multiple vaults.

Environment Variables vs .env Files

While some instructions suggest using .env files at the root of the mcp-server code, this approach doesn't work for multiple vaults since each needs different settings. Instead, configure environment variables directly in Claude Desktop's claude_desktop_config.json.

Available Environment Variables

The mcp-obsidian server supports these environment variables:

• OBSIDIAN_API_KEY - API key for vault access
• OBSIDIAN_HOST - Server host (typically 127.0.0.1)
• OBSIDIAN_PORT - Port number for the API
• OBSIDIAN_PROTOCOL - Either "http" or "https"

Configuration Steps

Step 1: Configure Local REST API Plugin in Each Vault

For each Obsidian vault:

1. Open the vault in Obsidian
2. Go to Settings → Community Plugins → Local REST API
3. Enable "Show advanced settings"
4. Disable the "Encrypted (HTTPS) Server" option
5. Set a unique "Non-encrypted (HTTP) Server Port" number for each vault
   • Example: Vault 1 uses port 27123, Vault 2 uses port 27125
   • Ensure ports don't conflict with other services
6. Generate and copy the API key for this vault

Security Note: This configuration uses HTTP instead of HTTPS for simplicity. HTTPS configuration with multiple vaults has not been tested yet. For production use, consider implementing HTTPS with proper certificates.

Step 2: Configure Claude Desktop

1. Locate Claude Desktop's configuration file:

   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • Windows: %APPDATA%\Claude\claude_desktop_config.json
   • Linux: ~/.config/Claude/claude_desktop_config.json

2. Add MCP server configurations for each vault:

{
  "mcpServers": {
    "obsidian-personal": {
      "command": "/opt/homebrew/bin/uv",
      "args": [
        "--directory",
        "/path/to/your/mcp-obsidian",
        "run",
        "mcp-obsidian"
      ],
      "env": {
        "OBSIDIAN_API_KEY": "your-api-key-for-first-vault",
        "OBSIDIAN_HOST": "127.0.0.1",
        "OBSIDIAN_PORT": "27123",
        "OBSIDIAN_PROTOCOL": "http"
      }
    },
    "obsidian-work": {
      "command": "/opt/homebrew/bin/uv",
      "args": [
        "--directory",
        "/path/to/your/mcp-obsidian",
        "run",
        "mcp-obsidian"
      ],
      "env": {
        "OBSIDIAN_API_KEY": "your-api-key-for-second-vault",
        "OBSIDIAN_HOST": "127.0.0.1",
        "OBSIDIAN_PORT": "27125",
        "OBSIDIAN_PROTOCOL": "http"
      }
    }
  },
  "globalShortcut": ""
}

3. Replace /path/to/your/mcp-obsidian with the actual path to your mcp-obsidian installation
4. Replace the API keys with the actual keys from each vault
5. Save the file

Step 3: Restart Claude Desktop

1. Restart Claude Desktop to load the new configuration
2. Verify vault connectivity: Obsidian does not need to be restarted - the Local REST API plugins will continue running
3. Confirm both vaults show the Local REST API plugin as active

Usage

Once configured, you can interact with specific vaults by referencing their MCP server names:

• "List all notes in obsidian-personal"
• "Search for project notes using obsidian-work"
• "Create a new note in obsidian-personal about today's meeting"

Claude Desktop will automatically route requests to the appropriate vault based on the MCP server name you specify.

Troubleshooting

Common Issues:

1. Connection refused errors:

   • Verify Obsidian is running and the Local REST API plugin is active
   • Check that the port numbers match between Obsidian and Claude Desktop config

2. API key authentication failures:

   • Copy the correct API key from the Local REST API plugin settings in Obsidian
   • Ensure API keys are correctly pasted into the configuration file without extra spaces

3. Port conflicts:

   • Use lsof -i :PORT_NUMBER on macOS/Linux to check if a port is in use
   • Choose different port numbers if conflicts exist

4. MCP server not found:

   • Verify the path to mcp-obsidian is correct in the configuration
   • Check that all required dependencies are installed
   • Monitor MCP server logs for detailed error information:

     tail -n 20 -f ~/Library/Logs/Claude/mcp-server-mcp-obsidian.log

Verification Steps:

1. Check Claude Desktop logs for connection errors

2. Verify the Local REST API plugin shows "Running" status in Obsidian

3. Test basic API connectivity using httpie:

   http :27123

   This should return a JSON response with service information and "status": "OK", confirming the REST server is running.

4. Test authenticated API access:

   http :27123/vault/ Authorization:"Bearer YOUR_API_KEY"

   Replace YOUR_API_KEY with the actual API key and 27123 with your configured port.

Security Considerations

• HTTP vs HTTPS: This guide uses HTTP for simplicity, but HTTPS is more secure
• API Key Protection: Keep API keys secure and don't share configuration files
• Network Access: The REST API only binds to localhost by default, limiting exposure

Future Improvements

• Test and document HTTPS configuration with multiple vaults

References

• [MCP Obsidian Server Documentation](https://github.com/your-repo/mcp-obsidian)
• [Local REST API Obsidian Plugin](https://github.com/coddingtonbear/obsidian-local-rest-api)
• [Original YouTube Tutorial](https://www.youtube.com/watch?v=VeTnndXyJQI)

[davidbajusz]

Thank you, @vlcinsky, for the comprehensive guidelines, these will be greatly helpful. One question before I dive in: is it absolutely necessary to clone the repo and use a local installation, or can I follow the "default" pattern (below) with multiple entries?

"mcp-obsidian-arbitraryName": { "command": "uvx", "args": [ "mcp-obsidian" ], "env": { "OBSIDIAN_API_KEY": "...", "OBSIDIAN_HOST": "127.0.0.1", "OBSIDIAN_PORT": "arbitraryPort" } } "mcp-obsidian-arbitraryName2": { ... } }

I imagine you're using the local installation to reduce the risk of using http (vs. https), but the Obsidian Local REST API seems to have all the knobs to set up custom ports through https, so in theory it should work...?

[vlcinsky]

@davidbajusz
There two "versions" of `mcp-obsidian:

• released one (which you call default), installable from pypi.org by pip install mcp-obsidian, uv tool install mcp-obsidian etc.
• development one, which is not published on pypi.org yet and needs special care

I was trying to use the released version of mcp-obsidian but it did not work for me. Claude Desktop was always complaining, that it cannot connect to port 27124 while my MCP configuration was setting port 27123. It was simply ignoring my port configuration. It turned out we run into issue #46.

Given issue is resolved in development version but not yet released.

So for our use case "Use with multiple obsidian vaults" we have to use the development version or wait until the fix for #46 is published in some new version on pypi.org.

Finally I ended with following setup:

Installing (latest) development version

Install development version using uv:

$ git clone git@github.com:MarkusPfundstein/mcp-obsidian.git
$ cd mcp-obsidian
$ uv tool install .

Now I have development version of mcp-obsidian available anywhere in my terminal.

To upgrade to the latest (development) version:

$ cd mcp-obsidian
$ git pull
$ uv tool uninstall mcp-obsidian
$ uv tool install .

To upgrade to the latest released version (wait until version > 0.2.2 is released):

$ uv tool uninstall mcp-obsidian
$ uv tool upgrade mcp-obsidian

Note: I could probably do diretly $ uv tool upgrade mcp-obsidian but I did not test it.

Finally I used following claude MCP configuration:

{
  "mcpServers": {
    "obsidian-vault1": {
      "command": "/Users/javl/.local/bin/mcp-obsidian",
      "env": {
        "OBSIDIAN_PORT": "27123",
        "OBSIDIAN_API_KEY": "proper-token-value-for-vault-1",
        "OBSIDIAN_HOST": "127.0.0.1",
        "OBSIDIAN_PROTOCOL": "http"
      }
    },
    "obsidian-vault2": {
      "command": "/Users/javl/.local/bin/mcp-obsidian",
      "env": {
        "OBSIDIAN_PORT": "27125",
        "OBSIDIAN_API_KEY": "proper-token-value-for-vault-2",
        "OBSIDIAN_HOST": "127.0.0.1",
        "OBSIDIAN_PROTOCOL": "http"
      }
   }
}

It is just an alternative for what is proposed in project README.md but not using uvx in the configuration as it is directly using the mcp-obsidian installed in the system.

Lessons learned

• until the fix for Is it possible to connect to a different Local REST API port other than Default 27124? #46 is released, to use multiple vaults we have to use development version
• there are multiple ways to install mcp-obsidian - even the develpoment version can be installed
• there are multiple ways to run mcp-obsidian:
  • uvx mcp-obsidian - but this is going to install (default) version released on pypi.org, not a development one
  • uv run mcp-obsidian - the same as above
  • mcp-obsidian - whichever version is installed, in configuration is safer to use full path
• mcp-obsidian does not provide simple method to check which version is installed (I created Add --version option #78), one has to use tricks such as uv tool list |grep mcp-obsidian.

[davidbajusz]

Thanks for the detailed explanations and instructions, @vlcinsky! Tried it, works like a charm. :)

[vlcinsky]

Check the #80 proposal for even simpler configuration by pointing to the folder with obsidian vault.