How to integrate Atlassian MCP with Claude Code

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Introduction

This guide shows you how to set up Atlassian with Claude Code. Once you're done, Claude Code will be able to connect to your Atlassian account and run operations from natural language instructions.

We'll use Composio MCP to make the integration smooth and secure. Composio handles Atlassian authentication, loads the right Atlassian tools as needed, and manages tool execution for you. The result is a setup where you can talk to Claude Code in plain English and have it interact with Atlassian, making common tasks faster and easier.

Before we dive in, let's take a quick look at the key ideas and tools involved.

TL;DR

Here's what you'll learn:
  • What is Atlassian MCP and what's possible with it
  • What is Claude Code and why use it
  • What is Composio Tool Router and why you need it
  • Installing Claude Code to your system
  • Getting Composio API Keys
  • Programmatically create a Composio MCP session with Atlassian
  • Configure MCP inside Claude Code

What is Claude Code?

Claude Code is Anthropic's command line developer tool that lets you use Claude directly inside your terminal. Instead of switching between your editor, browser, and chat, you can stay in your project folder and ask Claude to help you build, debug, refactor, and understand code right where you're working.

Key features include:

  • Terminal-Native Experience: Work with Claude directly in your command line without switching contexts
  • MCP Support: Built-in support for Model Context Protocol servers to extend Claude's capabilities
  • Project Context: Claude understands your project structure and can read, write, and modify files
  • Interactive Development: Ask questions, debug code, and get help in real-time while coding
  • Multi-Platform: Works on macOS, Linux, WSL, and Windows

What is the Atlassian MCP server, and what's possible with it?

The Atlassian MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Atlassian account. It provides structured and secure access to your Atlassian workspace, enabling your agent to streamline issue tracking, project planning, documentation, and agile workflows on your behalf.

  • Comprehensive issue tracking: Empower your agent to create, update, assign, or comment on Jira issues, making bug tracking and task management seamless.
  • Automated project planning: Let your agent organize sprints, manage boards, and update project timelines to keep your team on track.
  • Collaborative documentation management: Enable your agent to create, edit, and organize Confluence pages for efficient knowledge sharing and documentation.
  • Agile workflow automation: Have your agent transition issues, move tasks across boards, and automate repetitive workflow steps to boost productivity.
  • Insightful reporting and analytics: Ask your agent to generate project reports, velocity charts, or sprint summaries for better visibility and decision-making.

Supported Tools & Triggers

Tools
No tools available

What is the Composio tool router, and how does it fit here?

What is Tool Router?

Composio's Tool Router helps agents find the right tools for a task at runtime. You can plug in multiple toolkits (like Gmail, HubSpot, and GitHub), and the agent will identify the relevant app and action to complete multi-step workflows. This can reduce token usage and improve the reliability of tool calls. Read more here: Getting started with Tool Router

The tool router generates a secure MCP URL that your agents can access to perform actions.

How the Tool Router works

The Tool Router follows a three-phase workflow:

  1. Discovery: Searches for tools matching your task and returns relevant toolkits with their details.
  2. Authentication: Checks for active connections. If missing, creates an auth config and returns a connection URL via Auth Link.
  3. Execution: Executes the action using the authenticated connection.

Step-by-step Guide

Prerequisites

Before starting, make sure you have:
  • Claude Pro, Max, or API billing enabled Anthropic account
  • Composio API Key
  • A Atlassian account
  • Basic knowledge of Python or TypeScript

Install Claude Code

bash
# macOS, Linux, WSL
curl -fsSL https://claude.ai/install.sh | bash

# Windows PowerShell
irm https://claude.ai/install.ps1 | iex

# Windows CMD
curl -fsSL https://claude.ai/install.cmd -o install.cmd && install.cmd && del install.cmd

To install Claude Code, use one of the following methods based on your operating system:

Set up Claude Code

bash
cd your-project-folder
claude

Open a terminal, go to your project folder, and start Claude Code:

  • Claude Code will open in your terminal
  • Follow the prompts to sign in with your Anthropic account
  • Complete the authentication flow
  • Once authenticated, you can start using Claude Code
Claude Code initial setup showing sign-in prompt
Claude Code terminal after successful login

Set up environment variables

bash
COMPOSIO_API_KEY=your_composio_api_key_here
USER_ID=your_user_id_here

Create a .env file in your project root with the following variables:

  • COMPOSIO_API_KEY authenticates with Composio (get it from Composio dashboard)
  • USER_ID identifies the user for session management (use any unique identifier)

Install Composio library

pip install composio-core python-dotenv

Install the Composio Python library to create MCP sessions.

  • composio-core provides the core Composio functionality
  • python-dotenv loads environment variables from your .env file

Generate Composio MCP URL

import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
USER_ID = os.getenv("USER_ID")

composio_client = Composio(api_key=COMPOSIO_API_KEY)

composio_session = composio_client.create(
    user_id=USER_ID,
    toolkits=["atlassian"],
)

COMPOSIO_MCP_URL = composio_session.mcp.url

print(f"MCP URL: {COMPOSIO_MCP_URL}")
print(f"\nUse this command to add to Claude Code:")
print(f'claude mcp add --transport http atlassian-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"')

Create a script to generate a Composio MCP URL for Atlassian. This URL will be used to connect Claude Code to Atlassian.

What's happening:
  • We import the Composio client and load environment variables
  • Create a Composio instance with your API key
  • Call create() to create a Tool Router session for Atlassian
  • The returned mcp.url is the MCP server URL that Claude Code will use
  • The script prints this URL so you can copy it

Run the script and copy the MCP URL

python generate_mcp_url.py

Run your Python script to generate the MCP URL.

  • The script connects to Composio and creates a Tool Router session
  • It prints the MCP URL and the exact command you need to run
  • Copy the entire claude mcp add command from the output

Add Atlassian MCP to Claude Code

bash
claude mcp add --transport http atlassian-composio "YOUR_MCP_URL_HERE" --headers "X-API-Key:YOUR_COMPOSIO_API_KEY"

# Then restart Claude Code
exit
claude

In your terminal, add the MCP server using the command from the previous step. The command format is:

  • claude mcp add registers a new MCP server with Claude Code
  • --transport http specifies that this is an HTTP-based MCP server
  • The server name (atlassian-composio) is how you'll reference it
  • The URL points to your Composio Tool Router session
  • --headers includes your Composio API key for authentication

After running the command, close the current Claude Code session and start a new one for the changes to take effect.

Verify the installation

bash
claude mcp list

Check that your Atlassian MCP server is properly configured.

  • This command lists all MCP servers registered with Claude Code
  • You should see your atlassian-composio entry in the list
  • This confirms that Claude Code can now access Atlassian tools

If everything is wired up, you should see your atlassian-composio entry listed:

Claude Code MCP list showing the toolkit MCP server

Authenticate Atlassian

The first time you try to use Atlassian tools, you'll be prompted to authenticate.

  • Claude Code will detect that you need to authenticate with Atlassian
  • It will show you an authentication link
  • Open the link in your browser (or copy/paste it)
  • Complete the Atlassian authorization flow
  • Return to the terminal and start using Atlassian through Claude Code

Once authenticated, you can ask Claude Code to perform Atlassian operations in natural language. For example:

  • "Create a new Jira issue for a bug report"
  • "List all open tasks in my current sprint"
  • "Summarize recent project updates from Confluence"

Complete Code

Here's the complete code to get you started with Atlassian and Claude Code:

import os
from composio import Composio
from dotenv import load_dotenv

load_dotenv()

COMPOSIO_API_KEY = os.getenv("COMPOSIO_API_KEY")
USER_ID = os.getenv("USER_ID")

composio_client = Composio(api_key=COMPOSIO_API_KEY)

composio_session = composio_client.create(
    user_id=USER_ID,
    toolkits=["atlassian"],
)

COMPOSIO_MCP_URL = composio_session.mcp.url

print(f"MCP URL: {COMPOSIO_MCP_URL}")
print(f"\nUse this command to add to Claude Code:")
print(f'claude mcp add --transport http atlassian-composio "{COMPOSIO_MCP_URL}" --headers "X-API-Key:{COMPOSIO_API_KEY}"')

Conclusion

You've successfully integrated Atlassian with Claude Code using Composio's MCP server. Now you can interact with Atlassian directly from your terminal using natural language commands.

Key features of this setup:

  • Terminal-native experience without switching contexts
  • Natural language commands for Atlassian operations
  • Secure authentication through Composio's managed MCP
  • Tool Router for dynamic tool discovery and execution

Next steps:

  • Try asking Claude Code to perform various Atlassian operations
  • Add more toolkits to your Tool Router session for multi-app workflows
  • Integrate this setup into your development workflow for increased productivity

You can extend this by adding more toolkits, implementing custom workflows, or building automation scripts that leverage Claude Code's capabilities.

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FAQ

What are the differences in Tool Router MCP and Atlassian MCP?

With a standalone Atlassian MCP server, the agents and LLMs can only access a fixed set of Atlassian tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Atlassian and many other apps based on the task at hand, all through a single MCP endpoint.

Can I use Tool Router MCP with Claude Code?

Yes, you can. Claude Code fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Atlassian tools.

Can I manage the permissions and scopes for Atlassian while using Tool Router?

Yes, absolutely. You can configure which Atlassian scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

How safe is my data with Composio Tool Router?

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Atlassian data and credentials are handled as safely as possible.

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