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Atlassian MCP Server

PyPI version Python Support License: MIT Code Quality Dependency Security

MCP server for Atlassian Cloud (Confluence & Jira) with seamless OAuth 2.0 authentication. This server enables AI agents to help users document work in Confluence, manage Jira issues, and understand project context.

Features

  • Seamless OAuth 2.0 Flow: Automatic browser-based authentication with PKCE security
  • Modular Architecture: Specialized client classes for Jira, Confluence, and Service Desk operations
  • Selective Module Loading: Configure which modules to load using environment variables
  • Jira Integration: Search, create, and update issues; add comments; manage work
  • Confluence Integration: Search and read content for context understanding
  • Service Management: Access support tickets and requests
  • Automatic Token Management: Handles token refresh automatically
  • Minimal Permissions: Follows least privilege principle with only required scopes

Architecture

The server uses a modular architecture with specialized client classes:

  • BaseAtlassianClient: Core OAuth 2.0 authentication and HTTP request handling
  • JiraClient: Jira-specific operations (issues, projects, comments)
  • ConfluenceClient: Confluence-specific operations (pages, spaces, search)
  • ServiceDeskClient: Service Management operations (requests, approvals, Assets CMDB)

Each module can be independently enabled/disabled for optimal performance and security.

Use Cases

This MCP server is designed to help AI agents assist users with:

  • Work Documentation: Help document work progress and decisions in Confluence
  • Issue Management: Create, update, and track Jira issues based on conversations
  • Context Understanding: Read Confluence pages to understand project background
  • Time & Activity Logging: Track work activities and time spent on tasks
  • Service Requests: Access service management tickets for support context
  • Project Coordination: Search across Jira and Confluence for project information

OAuth App Setup

1. Create OAuth App

  1. Go to Atlassian Developer Console
  2. Click Create → OAuth 2.0 integration
  3. Enter your app name and accept the terms
  4. Set Callback URL to: http://localhost:8080/callback

2. Configure Required Scopes

IMPORTANT: You must add these exact scopes to your OAuth app before the MCP server can function properly.

Jira API Scopes

Navigate to Permissions → Jira API and add:

  • read:jira-work - Read issues, projects, and search
  • read:jira-user - Read user information
  • write:jira-work - Create and update issues

Confluence API Scopes

Navigate to Permissions → Confluence API and add:

  • read:page:confluence - Read page content (granular scope for v2 API)
  • read:space:confluence - Read space information (granular scope for v2 API)
  • write:page:confluence - Create and update pages (granular scope for v2 API)

Service Management API Scopes

Navigate to Permissions → Jira Service Management API and add:

  • read:servicedesk-request - Read service management requests
  • write:servicedesk-request - Create and update service management requests
  • manage:servicedesk-customer - Manage service desk customers and participants
  • read:knowledgebase:jira-service-management - Search knowledge base articles

User Identity API Scopes

Navigate to Permissions → User identity API and add:

  • read:me - User profile information

Core Scopes

These are typically available by default:

  • offline_access - Token refresh capability

3. Install App to Your Atlassian Site

After configuring scopes, you need to install the app to your Atlassian site:

  1. In your OAuth app, go to Authorization tab
  2. Use the Authorization URL generator to create an installation URL:
    • Select your configured scopes
    • Choose your Atlassian site from the dropdown
    • Click Generate URL
  3. Visit the generated URL in your browser to install the app to your site
  4. Grant permissions when prompted by Atlassian

Note: This step is required before the MCP server can access your Atlassian data. The app must be installed and authorized for your specific site.

4. Get Your Credentials

After installing the app:

  1. Go to Settings tab in your OAuth app
  2. Copy your Client ID and Client Secret
  3. Set the environment variables (see Configuration section below)

5. Scope Configuration Summary

Minimal Required (12 scopes):

read:jira-work
read:jira-user  
write:jira-work
read:page:confluence
read:space:confluence
write:page:confluence
read:servicedesk-request
write:servicedesk-request
manage:servicedesk-customer
read:knowledgebase:jira-service-management
read:me
offline_access

Optional (add only if needed):

write:servicedesk-request      # Only if creating service tickets
manage:* scopes                # Only for administrative operations

6. Troubleshooting Scopes

If you get scope-related errors:

  • "scope does not match": The scope isn't added to your OAuth app in Developer Console
  • "Current user not permitted": User lacks product-level permissions (contact your Atlassian admin)
  • "Unauthorized": Check that all required scopes are properly configured

Note: After adding new scopes to your OAuth app, you must re-authenticate using the authenticate_atlassian tool to get fresh tokens with the new permissions.

Installation

Prerequisites

  • Python 3.8 or higher
  • pip3 package manager
  • Access to an Atlassian Cloud site
  • OAuth app configured (see OAuth App Setup above)

Install from PyPI (Recommended)

pip3 install atlassian-mcp-server

Install from GitHub Repository

# Install directly from GitHub repository
pip3 install git+https://github.com/rorymcmahon/atlassian-mcp-server.git

Install from Source

# Clone the repository
git clone https://github.com/rorymcmahon/atlassian-mcp-server.git
cd atlassian-mcp-server

# Install in development mode
pip3 install -e .

Verify Installation

# Check that the command is available
atlassian-mcp-server --help

# Or check the Python module
python -m atlassian_mcp_server --help

Configuration

Set the following environment variables:

export ATLASSIAN_SITE_URL="https://your-domain.atlassian.net"
export ATLASSIAN_CLIENT_ID="your-oauth-client-id"
export ATLASSIAN_CLIENT_SECRET="your-oauth-client-secret"

Optional Configuration

Module Selection: Control which modules are loaded (default: all modules enabled):

export ATLASSIAN_MODULES="jira,confluence,service_desk"  # Enable specific modules
export ATLASSIAN_MODULES="jira,confluence"              # Enable only Jira and Confluence
export ATLASSIAN_MODULES="jira"                         # Enable only Jira

Available modules:

  • jira - Jira issue management and project operations
  • confluence - Confluence page and space operations
  • service_desk - Service Management and Assets CMDB operations

Note: Disabling unused modules reduces memory usage and improves startup time.

Usage

# Start the MCP server
python -m atlassian_mcp_server

# Or run directly
python src/atlassian_mcp_server/server.py

MCP Client Configuration

Note: All configuration examples below show the required environment variables. You can optionally add "ATLASSIAN_MODULES": "jira,confluence,service_desk" to any env section to control which modules are loaded.

Claude Desktop

Add to your Claude Desktop configuration file:

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

{
  "mcpServers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}

Amazon Q Developer CLI

Create an agent configuration file:

File: ~/.aws/amazonq/cli-agents/atlassian.json

{
  "$schema": "https://raw.githubusercontent.com/aws/amazon-q-developer-cli/refs/heads/main/schemas/agent-v1.json",
  "name": "atlassian",
  "description": "Atlassian Jira and Confluence integration agent",
  "prompt": "You are an AI assistant with access to Atlassian Jira and Confluence. Help users manage issues, search content, and document their work.",
  "mcpServers": {
    "atlassian-mcp-server": {
      "command": "atlassian-mcp-server",
      "args": [],
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      },
      "autoApprove": ["*"],
      "disabled": false,
      "timeout": 60000,
      "initTimeout": 120000
    }
  },
  "tools": [
    "@atlassian-mcp-server/*"
  ],
  "allowedTools": [
    "@atlassian-mcp-server/*"
  ]
}

Then use: q chat --agent atlassian

VS Code with Continue

Add to your Continue configuration:

File: ~/.continue/config.json

{
  "models": [...],
  "mcpServers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}

VS Code with GitHub Copilot Chat

For GitHub Copilot Chat with MCP support, add to workspace settings:

File: .vscode/settings.json

{
  "github.copilot.chat.mcp.servers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}

Cline (VS Code Extension)

Add to Cline's MCP configuration:

File: ~/.cline/mcp_servers.json

{
  "atlassian": {
    "command": "atlassian-mcp-server",
    "env": {
      "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
      "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
      "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
    }
  }
}

Environment Variables Setup

For security, set environment variables instead of hardcoding in config files:

# Add to your shell profile (.bashrc, .zshrc, etc.)
export ATLASSIAN_SITE_URL="https://your-domain.atlassian.net"
export ATLASSIAN_CLIENT_ID="your-oauth-client-id"
export ATLASSIAN_CLIENT_SECRET="your-oauth-client-secret"

Then use in configurations:

{
  "env": {
    "ATLASSIAN_SITE_URL": "${ATLASSIAN_SITE_URL}",
    "ATLASSIAN_CLIENT_ID": "${ATLASSIAN_CLIENT_ID}",
    "ATLASSIAN_CLIENT_SECRET": "${ATLASSIAN_CLIENT_SECRET}"
  }
}

Authentication Flow

  1. Start the MCP server
  2. Use the authenticate_atlassian tool to begin OAuth flow
  3. Browser opens automatically to Atlassian login
  4. After authorization, authentication completes automatically
  5. Credentials are saved locally for future use

Available Tools

Authentication

  • authenticate_atlassian() - Start seamless OAuth authentication flow

Jira Operations

  • jira_search(jql, max_results=50) - Search issues with JQL
  • jira_get_issue(issue_key) - Get specific issue details
  • jira_create_issue(project_key, summary, description, issue_type="Task") - Create new issue
  • jira_update_issue(issue_key, summary=None, description=None) - Update existing issue
  • jira_add_comment(issue_key, comment) - Add comment to issue

Confluence Operations

Core Content Management

  • confluence_search(query, limit=10) - Search Confluence content
  • confluence_get_page(page_id) - Get specific page content
  • confluence_create_page(space_key, title, content, parent_id=None) - Create new Confluence page
  • confluence_update_page(page_id, title, content, version) - Update existing Confluence page

Space Management

  • confluence_list_spaces(limit=25, space_type=None, status="current") - List available spaces
  • confluence_get_space(space_id, include_icon=False) - Get detailed space information
  • confluence_get_space_pages(space_id, limit=25, status="current") - Get pages in a space

Enhanced Search & Discovery

  • confluence_search_content(query, limit=25, space_id=None) - Advanced content search
  • confluence_get_page_children(page_id, limit=25) - Get child pages

Comments & Collaboration

  • confluence_get_page_comments(page_id, limit=25) - Get page comments
  • confluence_add_comment(page_id, comment, parent_comment_id=None) - Add comment to page
  • confluence_get_comment(comment_id) - Get specific comment details

Labels & Organization

  • confluence_get_page_labels(page_id, limit=25) - Get labels for a page
  • confluence_search_by_label(label_id, limit=25) - Find pages with specific label
  • confluence_list_labels(limit=25, prefix=None) - List all available labels

Attachments

  • confluence_get_page_attachments(page_id, limit=25) - Get page attachments
  • confluence_get_attachment(attachment_id) - Get attachment details

Version History

  • confluence_get_page_versions(page_id, limit=25) - Get page version history
  • confluence_get_page_version(page_id, version_number) - Get specific page version

Service Management Operations

Discovery Tools (Essential for AI Agents)

  • servicedesk_check_availability() - Check if Jira Service Management is configured
  • servicedesk_list_service_desks(limit=50) - List available service desks for creating requests
  • servicedesk_get_service_desk(service_desk_id) - Get detailed service desk information
  • servicedesk_list_request_types(service_desk_id=None, limit=50) - List available request types
  • servicedesk_get_request_type(service_desk_id, request_type_id) - Get detailed request type information
  • servicedesk_get_request_type_fields(service_desk_id, request_type_id) - Get required/optional fields for request type

Request Management

  • servicedesk_get_requests(service_desk_id=None, limit=50) - Get service desk requests
  • servicedesk_get_request(issue_key) - Get specific service desk request details
  • servicedesk_create_request(service_desk_id, request_type_id, summary, description) - Create new service request
  • servicedesk_add_comment(issue_key, comment, public=True) - Add comment to service request
  • servicedesk_get_request_comments(issue_key, limit=50) - Get comments for a service request
  • servicedesk_get_request_status(issue_key) - Get service request status
  • servicedesk_get_request_transitions(issue_key) - Get available status transitions for request
  • servicedesk_transition_request(issue_key, transition_id, comment=None) - Transition request to new status

Approval & Participant Management

  • servicedesk_get_approvals(issue_key) - Get approval information for request
  • servicedesk_approve_request(issue_key, approval_id, decision) - Approve or decline request approval
  • servicedesk_get_participants(issue_key) - Get participants for request
  • servicedesk_add_participants(issue_key, usernames) - Add participants to request (with confirmation prompts)
  • servicedesk_manage_notifications(issue_key, subscribe) - Subscribe/unsubscribe from request notifications

Troubleshooting

Authentication Issues

  • Ensure redirect URI matches exactly: http://localhost:8080/callback
  • Check that all required scopes are configured in Atlassian Developer Console
  • Verify environment variables are set correctly

Permission Issues

  • Ensure your user has appropriate Jira and Confluence access
  • Check that OAuth app has all required scopes enabled
  • Verify user is in correct groups (e.g., confluence-users)

API Errors

  • Check that your Atlassian site URL is correct
  • Ensure you have proper permissions for the resources you're accessing
  • Run the test scripts to verify functionality

Scope Requirements

This MCP server uses minimal required scopes following the principle of least privilege:

Essential Scopes (16 total)

  • Jira: read:jira-work, read:jira-user, write:jira-work
  • Confluence: read:page:confluence, read:space:confluence, write:page:confluence, read:comment:confluence, write:comment:confluence, read:label:confluence, read:attachment:confluence
  • Service Management: read:servicedesk-request, write:servicedesk-request, manage:servicedesk-customer, read:knowledgebase:jira-service-management
  • Core: read:me, offline_access

Optional Scopes (add only if needed)

  • manage:* scopes - Only for administrative operations

Important: Granular Scopes for v2 API

This MCP server uses granular scopes for Confluence operations to ensure compatibility with Confluence v2 API endpoints. The v2 API provides better performance and future-proofing compared to the deprecated v1 REST API.

Granular vs Classic Scopes:

  • Granular (recommended): read:page:confluence, write:page:confluence - Works with v2 API
  • Classic (deprecated): read:confluence-content.all, write:confluence-content - Only works with v1 API

If you previously configured classic scopes, you'll need to update your OAuth app to use granular scopes and re-authenticate to get fresh tokens.

Supply Chain Security

This project implements comprehensive supply chain security measures:

Dependency Management

  • Pinned Versions: All dependencies use exact version pins to prevent unexpected updates
  • Security Scanning: Automated vulnerability scanning with Safety and pip-audit
  • Dependency Tracking: Complete dependency documentation in docs/DEPENDENCIES.md
  • Regular Updates: Weekly automated security checks via GitHub Actions

Security Tools

# Generate dependency report
python3 scripts/generate_dependency_report.py

# Check for vulnerabilities
pip3 install safety pip-audit
safety check
pip-audit

# Update dependencies safely
python3 scripts/update_dependencies.py

Files

  • requirements.txt - Pinned production dependencies
  • docs/DEPENDENCIES.md - Human-readable dependency report
  • docs/dependency-report.json - Machine-readable dependency data
  • SECURITY.md - Security policy and vulnerability response
  • .github/workflows/dependency-security.yml - Automated security checks

Development

The server is built using:

  • FastMCP: Modern MCP server framework
  • httpx: Async HTTP client
  • Pydantic: Data validation and settings management

License

MIT License - see LICENSE file for details.

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MCP server for Atlassian Cloud (Confluence & Jira) with OAuth authentication

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v0.4.4 Latest
Mar 21, 2026
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