Connecting AI Tools to Obsidian with MCP Server - Gemini CLI & Kiro Guide

The demand for integrating AI tools with Obsidian has been growing rapidly. Today, I'll show you how to use MCP (Model Context Protocol) server to directly control Obsidian notes from Gemini CLI and Kiro.

After testing this setup myself, I found it incredibly convenient to search and create Obsidian notes using natural language. I'll cover everything including how to access Windows Obsidian from WSL environment.

What is MCP Server?

MCP (Model Context Protocol) server acts as a bridge between AI tools and external applications. Simply put, it enables AI tools like Gemini CLI and Kiro to control Obsidian using natural language commands.

Think of it as a translator that converts instructions like "search today's notes" or "create a new note" into actual Obsidian operations.

Setting Up Obsidian

Enable Community Plugins

First, let's enable community plugins in Obsidian:

1. Open Obsidian settings
2. Navigate to "Community plugins"
3. Click "Turn on community plugins"

Install Local REST API Plugin

Next, we need to enable external access to Obsidian through an API:

1. Search for "Local REST API" in community plugins
2. Install and enable the plugin
3. Note down the API Key shown in the settings

Make sure to save this API Key as we'll need it for CLI integration later.

Install MCP Tools Plugin

Now let's install the MCP server itself:

1. Search and install "MCP Tools" plugin
2. After enabling, click "Install server"
3. The MCP server executable mcp-server will be placed in your vault

Path Configuration

Getting the Execution Path

From the plugin settings, open the "Server install folder" and navigate to the bin folder to get the path.

Important: You need to manually append /mcp-server to the folder path.

Example (Windows environment):

C:/Users/username/OneDrive/tools/obsidian/.obsidian/plugins/mcp-tools/bin/mcp-server

Handling Paths with Spaces

If your path contains spaces (like Obsidian Vault), always wrap it in double quotes when using in terminal commands.

Gemini CLI Configuration

Registering the MCP Server

Run the following command in your terminal:

gemini mcp add obsidian-mcp-tools -s user -- "path/to/mcp-server" --env OBSIDIAN_API_KEY="your_api_key"

Real example:

gemini mcp add obsidian-mcp-tools -s user -- "C:/Users/username/OneDrive/tools/obsidian/.obsidian/plugins/mcp-tools/bin/mcp-server" --env OBSIDIAN_API_KEY="your_api_key"

The -s user option makes the server available across all projects.

Direct Configuration File Editing

If you prefer editing configuration files directly, you can add this to ~/.gemini/settings.json:

{
  "mcpServers": {
    "obsidian-mcp-tools": {
      "command": "C:/Users/username/OneDrive/tools/obsidian/.obsidian/plugins/mcp-tools/bin/mcp-server",
      "args": [],
      "env": {
        "OBSIDIAN_API_KEY": "your_api_key"
      }
    }
  }
}

Verify Connection

Once configured, verify the connection:

gemini mcp list

You should see something like:

obsidian-mcp-tools: ... - ✓ Connected

Testing the Setup

Getting Note List

Start Gemini and test Obsidian operations:

gemini

In the chat interface, try:

Get the list of notes in Obsidian

If everything is set up correctly, you should see your Obsidian notes listed.

Other Operation Examples

You can now use natural language commands like:

• "Create a new note"
• "Search for notes with specific keywords"
• "Read the content of a note"

WSL to Windows Obsidian Connection

For WSL users, here's how to access Windows Obsidian from Linux environment.

Kiro Configuration

1. Open Kiro
2. Add the following to your MCP server configuration:

{
  "mcpServers": {
    "mcp-obsidian": {
      "command": "npx",
      "args": [
        "-y",
        "@smithery/cli@latest",
        "run",
        "mcp-obsidian",
        "--config",
        "{\"vaultPath\":\"/mnt/c/Users/username/OneDrive/tools/obsidian\"}"
      ],
      "env": {},
      "disabled": false,
      "autoApprove": [
        "search_notes",
        "read_notes"
      ]
    }
  }
}

The key is converting Windows paths to WSL mount paths (/mnt/c/...).

Note: The smithery-ai approach is simpler to configure but only supports reading notes, not writing.

Troubleshooting

Common Issues and Solutions

Connection Problems

• Verify API Key is correctly set
• Ensure Obsidian is running
• Wrap paths with spaces in quotes

WSL Connection Issues

• Confirm Windows Obsidian is running
• Verify path is correctly mounted (/mnt/c/...)

Conclusion

Using Obsidian MCP server enables direct control of Obsidian from AI tools. This is particularly valuable for users managing large collections of notes, as natural language search and operations become possible.

The ability to access Windows Obsidian from WSL environments makes this solution versatile across different development setups.

Give it a try and experience more efficient note management. If you encounter any issues, double-check your configuration settings.