Atlassian MCP

A custom Model Context Protocol server that lets AI agents interact with Jira and Confluence on Atlassian Cloud. It makes plain REST calls in the background using the Jira REST API v3 and the Confluence REST API v2.

Setup

1. Install dependencies and build:

   npm install
   npm run build

2. Expose the server as a global command so it can be launched from any workspace (uses the bin entry in package.json):

   npm link

   This puts an atlassian-mcp command on your PATH. Re-run npm run build after code changes; the linked command always points at the current dist.

3. Create an API token at https://id.atlassian.com/manage-profile/security/api-tokens.

4. Provide credentials via environment variables (see .env.example):

   Variable	Description
   ATLASSIAN_SITE_URL	Your site, e.g. https://your-domain.atlassian.net
   ATLASSIAN_EMAIL	The email of your Atlassian account
   ATLASSIAN_API_TOKEN	The API token created above

Related MCP server: jira-mcp

Connecting a client

VS Code (recommended)

This repo ships a standard .vscode/mcp.json. It launches the server through a login + interactive zsh (zsh -lic) so it inherits the Atlassian credentials exported in your ~/.zshrc (or ~/.zshenv) — no secrets in the config — and calls the globally linked atlassian-mcp command so it works regardless of which repo is open:

{
  "servers": {
    "atlassian": {
      "type": "stdio",
      "command": "zsh",
      "args": ["-lic", "exec atlassian-mcp"]
    }
  }
}

Avoid ${workspaceFolder} here: it resolves to whatever repo is currently open, so it would break when the server is used from other workspaces. The npm link command name is resolved from your shell PATH instead.

To make the server available in every workspace, add the same servers block to your user-level MCP config (Command Palette → MCP: Open User Configuration).

Alternative: run node with an absolute path

If you'd rather not npm link, point node directly at the built entry file using an absolute path (not ${workspaceFolder}, which changes per workspace). VS Code's ${userHome} variable keeps it portable across machines:

{
  "servers": {
    "atlassian": {
      "type": "stdio",
      "command": "zsh",
      "args": ["-lic", "exec node \"${userHome}/Sites/atlassian-mcp/dist/index.js\""]
    }
  }
}

Adjust the path if you cloned the repo elsewhere. The zsh -lic wrapper still supplies the credentials from your shell profile.

Export the variables in your shell profile instead of the config file:

export ATLASSIAN_SITE_URL="https://your-domain.atlassian.net"
export ATLASSIAN_EMAIL="you@example.com"
export ATLASSIAN_API_TOKEN="your-api-token"

Reload the VS Code window after changing your shell profile so the new values are picked up.

Other clients (Claude Desktop, Cline, Cursor)

Clients that don't run through your shell can either use the same zsh -lic wrapper or set the variables explicitly:

{
  "mcpServers": {
    "atlassian": {
      "command": "atlassian-mcp",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_EMAIL": "you@example.com",
        "ATLASSIAN_API_TOKEN": "your-api-token"
      }
    }
  }
}

Without npm link, use node with an absolute path to the built entry file:

{
  "mcpServers": {
    "atlassian": {
      "command": "node",
      "args": ["/absolute/path/to/atlassian-mcp/dist/index.js"],
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_EMAIL": "you@example.com",
        "ATLASSIAN_API_TOKEN": "your-api-token"
      }
    }
  }
}

For local development you can run the server directly with npm run dev.

Tools

Jira

Confluence

Notes

• Jira rich-text fields (descriptions, comments) accept plain text, which is converted to Atlassian Document Format (ADF) automatically.

• Confluence page/comment bodies use storage format (XHTML), e.g. <p>Hi</p>.

• Your API token inherits all permissions of your account. Keep it secret and never commit it.