How to configure environment variables for MCP servers

Each MCP host stores its server configuration in a specific JSON file. Claude Desktop on macOS uses ~/Library/Application Support/Claude/claude_desktop_config.json. On Windows, it is %APPDATA%\Claude\claude_desktop_config.json. Cursor uses .cursor/mcp.json in your project directory for project-scoped servers, or ~/.cursor/mcp.json for global servers. Open this file in any text editor.

1# Claude Desktop config location
2# macOS:
3~/Library/Application Support/Claude/claude_desktop_config.json
4
5# Windows:
6%APPDATA%\Claude\claude_desktop_config.json
7
8# Cursor config location
9# Project-scoped:
10.cursor/mcp.json
11
12# Global:
13~/.cursor/mcp.json

Inside your server definition, add an env object with key-value pairs for each environment variable. The keys become environment variable names and the values are their contents. These variables are set in the server process environment when the host starts the server. This is the correct and secure way to pass API keys — never put them directly in your server's source code.

1{
2  "mcpServers": {
3    "my-server": {
4      "command": "node",
5      "args": ["./dist/index.js"],
6      "env": {
7        "API_KEY": "sk-your-api-key-here",
8        "DATABASE_URL": "postgresql://user:pass@localhost:5432/mydb",
9        "LOG_LEVEL": "debug"
10      }
11    }
12  }
13}

In your MCP server, read environment variables using the standard approach for your language. In TypeScript/Node.js, use process.env.VARIABLE_NAME. In Python, use os.environ["VARIABLE_NAME"] or os.environ.get("VARIABLE_NAME", "default"). Always validate that required variables are present at startup and fail with a clear error message if they are missing.

1// TypeScript — reading env vars in your MCP server
2const apiKey = process.env.API_KEY;
3if (!apiKey) {
4  console.error("ERROR: API_KEY environment variable is not set");
5  console.error("Add it to your MCP host config under the env block");
6  process.exit(1);
7}
8
9// Python — reading env vars
10import os
11import sys
12
13api_key = os.environ.get("API_KEY")
14if not api_key:
15    print("ERROR: API_KEY environment variable is not set", file=sys.stderr)
16    sys.exit(1)

Many community MCP servers are distributed as npm packages and run via npx. You configure environment variables the same way — add an env block alongside the command and args fields. The environment variables are passed to the npx child process which forwards them to the server. This is how you configure servers you did not write, like @modelcontextprotocol/server-github or @modelcontextprotocol/server-slack.

1{
2  "mcpServers": {
3    "github": {
4      "command": "npx",
5      "args": ["-y", "@modelcontextprotocol/server-github"],
6      "env": {
7        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_your_token_here"
8      }
9    },
10    "slack": {
11      "command": "npx",
12      "args": ["-y", "@modelcontextprotocol/server-slack"],
13      "env": {
14        "SLACK_BOT_TOKEN": "xoxb-your-token",
15        "SLACK_TEAM_ID": "T01234567"
16      }
17    }
18  }
19}

After editing the configuration file, you must restart your MCP host for the changes to take effect. Claude Desktop requires a full application restart — quit and reopen it. Cursor typically picks up changes when you reload the window (Cmd+Shift+P then Reload Window), though a full restart is more reliable. Verify the connection by checking that the server's tools appear in your host. If you manage multiple MCP servers with complex configurations and need help streamlining the setup, the RapidDev team can help architect a clean configuration.