Mcp Atlassian

What is Mcp Atlassian about?

Mcp Atlassian delivers a server that bridges AI assistants with Atlassian tools, allowing natural‑language queries and commands to read, search, create, and update content in Confluence and Jira.

How to use Mcp Atlassian?

1. Install the Docker image or run the npm package via npx.
2. Configure authentication (API token, personal access token, or OAuth 2.0) through environment variables or an .env file.
3. Start the server with the desired transport (stdio, sse, or streamable‑http).
4. Connect your IDE or AI assistant to the server using the generated MCP endpoint.

Key features of Mcp Atlassian

• Full support for Confluence Cloud, Confluence Server/Data‑Center, Jira Cloud, and Jira Server/Data‑Center.
• Three authentication methods: API token (cloud), personal access token (server/DC), and OAuth 2.0 (cloud).
• Rich toolset covering read‑only operations (search, get, list) and write operations (create, update, comment, transition).
• Fine‑grained tool filtering via ENABLED_TOOLS and read‑only mode.
• Proxy and custom HTTP header support for corporate environments.
• Multi‑cloud OAuth mode for per‑user tokens in multi‑tenant applications.

Use cases of Mcp Atlassian

• Automated meeting minutes: Extract action items from notes and create Jira issues instantly.
• AI‑powered knowledge search: Ask natural‑language questions and retrieve summarized Confluence pages.
• Smart issue triage: Filter and list urgent bugs based on JQL queries.
• Content generation: Draft design documents or project pages directly from prompts.
• Enterprise integrations: Embed Atlassian data in chatbots, internal tools, or CI/CD pipelines.

FAQ for Mcp Atlassian

Q: Which authentication method should I choose? A: For cloud deployments, API token is the simplest. Use OAuth 2.0 for enterprise‑grade security or when multiple users need separate tokens. For server/DC, use a personal access token.

Q: Do I need to run the Docker image? A: Docker is the recommended distribution, but the server can also be launched via npx mcp-atlassian for quick testing.

Q: Can I limit which tools are exposed? A: Yes. Set ENABLED_TOOLS (or --enabled-tools) to a comma‑separated list, and enable READ_ONLY_MODE to restrict to read operations.

Q: How do I handle self‑signed certificates? A: Set CONFLUENCE_SSL_VERIFY=false or JIRA_SSL_VERIFY=false in the environment.

Q: Is there support for multi‑tenant OAuth? A: Yes. Enable ATLASSIAN_OAUTH_ENABLE=true and provide per‑request Authorization and X-Atlassian-Cloud-Id headers.

MCP Atlassian

Model Context Protocol (MCP) server for Atlassian products (Confluence and Jira). This integration supports both Confluence & Jira Cloud and Server/Data Center deployments.

Example Usage

Ask your AI assistant to:

• 📝 Automatic Jira Updates - "Update Jira from our meeting notes"
• 🔍 AI-Powered Confluence Search - "Find our OKR guide in Confluence and summarize it"
• 🐛 Smart Jira Issue Filtering - "Show me urgent bugs in PROJ project from last week"
• 📄 Content Creation & Management - "Create a tech design doc for XYZ feature"

Feature Demo

https://github.com/user-attachments/assets/35303504-14c6-4ae4-913b-7c25ea511c3e

https://github.com/user-attachments/assets/7fe9c488-ad0c-4876-9b54-120b666bb785

Compatibility

Product	Deployment Type	Support Status
Confluence	Cloud	✅ Fully supported
Confluence	Server/Data Center	✅ Supported (version 6.0+)
Jira	Cloud	✅ Fully supported
Jira	Server/Data Center	✅ Supported (version 8.14+)

Quick Start Guide

🔐 1. Authentication Setup

MCP Atlassian supports three authentication methods:

A. API Token Authentication (Cloud) - Recommended

1. Go to https://id.atlassian.com/manage-profile/security/api-tokens
2. Click Create API token, name it
3. Copy the token immediately

B. Personal Access Token (Server/Data Center)

1. Go to your profile (avatar) → Profile → Personal Access Tokens
2. Click Create token, name it, set expiry
3. Copy the token immediately

C. OAuth 2.0 Authentication (Cloud) - Advanced

[!NOTE] OAuth 2.0 is more complex to set up but provides enhanced security features. For most users, API Token authentication (Method A) is simpler and sufficient.

1. Go to Atlassian Developer Console
2. Create an "OAuth 2.0 (3LO) integration" app
3. Configure Permissions (scopes) for Jira/Confluence
4. Set Callback URL (e.g., http://localhost:8080/callback)
5. Run setup wizard:

   docker run --rm -i \
     -p 8080:8080 \
     -v "${HOME}/.mcp-atlassian:/home/app/.mcp-atlassian" \
     ghcr.io/sooperset/mcp-atlassian:latest --oauth-setup -v
   

6. Follow prompts for Client ID, Secret, URI, and Scope
7. Complete browser authorization
8. Add obtained credentials to .env or IDE config:
   • ATLASSIAN_OAUTH_CLOUD_ID (from wizard)
   • ATLASSIAN_OAUTH_CLIENT_ID
   • ATLASSIAN_OAUTH_CLIENT_SECRET
   • ATLASSIAN_OAUTH_REDIRECT_URI
   • ATLASSIAN_OAUTH_SCOPE

[!IMPORTANT] For the standard OAuth flow described above, include offline_access in your scope (e.g., read:jira-work write:jira-work offline_access). This allows the server to refresh the access token automatically.

If you are running mcp-atlassian part of a larger system that manages Atlassian OAuth 2.0 access tokens externally (e.g., through a central identity provider or another application), you can provide an access token directly to this MCP server. This method bypasses the interactive setup wizard and the server's internal token management (including refresh capabilities).

Requirements:

• A valid Atlassian OAuth 2.0 Access Token with the necessary scopes for the intended operations.
• The corresponding ATLASSIAN_OAUTH_CLOUD_ID for your Atlassian instance.

Configuration: To use this method, set the following environment variables (or use the corresponding command-line flags when starting the server):

• ATLASSIAN_OAUTH_CLOUD_ID: Your Atlassian Cloud ID. (CLI: --oauth-cloud-id)
• ATLASSIAN_OAUTH_ACCESS_TOKEN: Your pre-existing OAuth 2.0 access token. (CLI: --oauth-access-token)

Important Considerations for BYOT:

• Token Lifecycle Management: When using BYOT, the MCP server does not handle token refresh. The responsibility for obtaining, refreshing (before expiry), and revoking the access token lies entirely with you or the external system providing the token.
• Unused Variables: The standard OAuth client variables (ATLASSIAN_OAUTH_CLIENT_ID, ATLASSIAN_OAUTH_CLIENT_SECRET, ATLASSIAN_OAUTH_REDIRECT_URI, ATLASSIAN_OAUTH_SCOPE) are not used and can be omitted when configuring for BYOT.
• No Setup Wizard: The --oauth-setup wizard is not applicable and should not be used for this approach.
• No Token Cache Volume: The Docker volume mount for token storage (e.g., -v "${HOME}/.mcp-atlassian:/home/app/.mcp-atlassian") is also not necessary if you are exclusively using the BYOT method, as no tokens are stored or managed by this server.
• Scope: The provided access token must already have the necessary permissions (scopes) for the Jira/Confluence operations you intend to perform.

This option is useful in scenarios where OAuth credential management is centralized or handled by other infrastructure components.

[!TIP] Multi-Cloud OAuth Support: If you're building a multi-tenant application where users provide their own OAuth tokens, see the Multi-Cloud OAuth Support section for minimal configuration setup.

📦 2. Installation

MCP Atlassian is distributed as a Docker image. This is the recommended way to run the server, especially for IDE integration. Ensure you have Docker installed.

# Pull Pre-built Image
docker pull ghcr.io/sooperset/mcp-atlassian:latest

🛠️ IDE Integration

MCP Atlassian is designed to be used with AI assistants through IDE integration.

[!TIP] For Claude Desktop: Locate and edit the configuration file directly:

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

For Cursor: Open Settings → MCP → + Add new global MCP server

⚙️ Configuration Methods

There are two main approaches to configure the Docker container:

1. Passing Variables Directly (shown in examples below)
2. Using an Environment File with --env-file flag (shown in collapsible sections)

[!NOTE] Common environment variables include:

• CONFLUENCE_SPACES_FILTER: Filter by space keys (e.g., "DEV,TEAM,DOC")
• JIRA_PROJECTS_FILTER: Filter by project keys (e.g., "PROJ,DEV,SUPPORT")
• READ_ONLY_MODE: Set to "true" to disable write operations
• MCP_VERBOSE: Set to "true" for more detailed logging
• MCP_LOGGING_STDOUT: Set to "true" to log to stdout instead of stderr
• ENABLED_TOOLS: Comma-separated list of tool names to enable (e.g., "confluence_search,jira_get_issue")

See the .env.example file for all available options.

📝 Configuration Examples

Method 1 (Passing Variables Directly):

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e", "CONFLUENCE_URL",
        "-e", "CONFLUENCE_USERNAME",
        "-e", "CONFLUENCE_API_TOKEN",
        "-e", "JIRA_URL",
        "-e", "JIRA_USERNAME",
        "-e", "JIRA_API_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "CONFLUENCE_USERNAME": "your.email@company.com",
        "CONFLUENCE_API_TOKEN": "your_confluence_api_token",
        "JIRA_URL": "https://your-company.atlassian.net",
        "JIRA_USERNAME": "your.email@company.com",
        "JIRA_API_TOKEN": "your_jira_api_token"
      }
    }
  }
}

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "--env-file",
        "/path/to/your/mcp-atlassian.env",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ]
    }
  }
}

For Server/Data Center deployments, use direct variable passing:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "CONFLUENCE_URL",
        "-e", "CONFLUENCE_PERSONAL_TOKEN",
        "-e", "CONFLUENCE_SSL_VERIFY",
        "-e", "JIRA_URL",
        "-e", "JIRA_PERSONAL_TOKEN",
        "-e", "JIRA_SSL_VERIFY",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "CONFLUENCE_URL": "https://confluence.your-company.com",
        "CONFLUENCE_PERSONAL_TOKEN": "your_confluence_pat",
        "CONFLUENCE_SSL_VERIFY": "false",
        "JIRA_URL": "https://jira.your-company.com",
        "JIRA_PERSONAL_TOKEN": "your_jira_pat",
        "JIRA_SSL_VERIFY": "false"
      }
    }
  }
}

[!NOTE] Set CONFLUENCE_SSL_VERIFY and JIRA_SSL_VERIFY to "false" only if you have self-signed certificates.

These examples show how to configure mcp-atlassian in your IDE (like Cursor or Claude Desktop) when using OAuth 2.0 for Atlassian Cloud.

Example for Standard OAuth 2.0 Flow (using Setup Wizard):

This configuration is for when you use the server's built-in OAuth client and have completed the OAuth setup wizard.

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-v", "<path_to_your_home>/.mcp-atlassian:/home/app/.mcp-atlassian",
        "-e", "JIRA_URL",
        "-e", "CONFLUENCE_URL",
        "-e", "ATLASSIAN_OAUTH_CLIENT_ID",
        "-e", "ATLASSIAN_OAUTH_CLIENT_SECRET",
        "-e", "ATLASSIAN_OAUTH_REDIRECT_URI",
        "-e", "ATLASSIAN_OAUTH_SCOPE",
        "-e", "ATLASSIAN_OAUTH_CLOUD_ID",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "JIRA_URL": "https://your-company.atlassian.net",
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "ATLASSIAN_OAUTH_CLIENT_ID": "YOUR_OAUTH_APP_CLIENT_ID",
        "ATLASSIAN_OAUTH_CLIENT_SECRET": "YOUR_OAUTH_APP_CLIENT_SECRET",
        "ATLASSIAN_OAUTH_REDIRECT_URI": "http://localhost:8080/callback",
        "ATLASSIAN_OAUTH_SCOPE": "read:jira-work write:jira-work read:confluence-content.all write:confluence-content offline_access",
        "ATLASSIAN_OAUTH_CLOUD_ID": "YOUR_CLOUD_ID_FROM_SETUP_WIZARD"
      }
    }
  }
}

[!NOTE]

• For the Standard Flow:
  • ATLASSIAN_OAUTH_CLOUD_ID is obtained from the --oauth-setup wizard output or is known for your instance.
  • Other ATLASSIAN_OAUTH_* client variables are from your OAuth app in the Atlassian Developer Console.
  • JIRA_URL and CONFLUENCE_URL for your Cloud instances are always required.
  • The volume mount (-v .../.mcp-atlassian:/home/app/.mcp-atlassian) is crucial for persisting the OAuth tokens obtained by the wizard, enabling automatic refresh.

Example for Pre-existing Access Token (BYOT - Bring Your Own Token):

This configuration is for when you are providing your own externally managed OAuth 2.0 access token.

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "JIRA_URL",
        "-e", "CONFLUENCE_URL",
        "-e", "ATLASSIAN_OAUTH_CLOUD_ID",
        "-e", "ATLASSIAN_OAUTH_ACCESS_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "JIRA_URL": "https://your-company.atlassian.net",
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "ATLASSIAN_OAUTH_CLOUD_ID": "YOUR_KNOWN_CLOUD_ID",
        "ATLASSIAN_OAUTH_ACCESS_TOKEN": "YOUR_PRE_EXISTING_OAUTH_ACCESS_TOKEN"
      }
    }
  }
}

[!NOTE]

• For the BYOT Method:
  • You primarily need JIRA_URL, CONFLUENCE_URL, ATLASSIAN_OAUTH_CLOUD_ID, and ATLASSIAN_OAUTH_ACCESS_TOKEN.
  • Standard OAuth client variables (ATLASSIAN_OAUTH_CLIENT_ID, CLIENT_SECRET, REDIRECT_URI, SCOPE) are not used.
  • Token lifecycle (e.g., refreshing the token before it expires and restarting mcp-atlassian) is your responsibility, as the server will not refresh BYOT tokens.

MCP Atlassian supports routing API requests through standard HTTP/HTTPS/SOCKS proxies. Configure using environment variables:

• Supports standard HTTP_PROXY, HTTPS_PROXY, NO_PROXY, SOCKS_PROXY.
• Service-specific overrides are available (e.g., JIRA_HTTPS_PROXY, CONFLUENCE_NO_PROXY).
• Service-specific variables override global ones for that service.

Add the relevant proxy variables to the args (using -e) and env sections of your MCP configuration:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e", "... existing Confluence/Jira vars",
        "-e", "HTTP_PROXY",
        "-e", "HTTPS_PROXY",
        "-e", "NO_PROXY",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "... existing Confluence/Jira vars": "...",
        "HTTP_PROXY": "http://proxy.internal:8080",
        "HTTPS_PROXY": "http://proxy.internal:8080",
        "NO_PROXY": "localhost,.your-company.com"
      }
    }
  }
}

Credentials in proxy URLs are masked in logs. If you set NO_PROXY, it will be respected for requests to matching hosts.

MCP Atlassian supports adding custom HTTP headers to all API requests. This feature is particularly useful in corporate environments where additional headers are required for security, authentication, or routing purposes.

Custom headers are configured using environment variables with comma-separated key=value pairs:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "-e", "CONFLUENCE_URL",
        "-e", "CONFLUENCE_USERNAME",
        "-e", "CONFLUENCE_API_TOKEN",
        "-e", "CONFLUENCE_CUSTOM_HEADERS",
        "-e", "JIRA_URL",
        "-e", "JIRA_USERNAME",
        "-e", "JIRA_API_TOKEN",
        "-e", "JIRA_CUSTOM_HEADERS",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "CONFLUENCE_USERNAME": "your.email@company.com",
        "CONFLUENCE_API_TOKEN": "your_confluence_api_token",
        "CONFLUENCE_CUSTOM_HEADERS": "X-Confluence-Service=mcp-integration,X-Custom-Auth=confluence-token,X-ALB-Token=secret-token",
        "JIRA_URL": "https://your-company.atlassian.net",
        "JIRA_USERNAME": "your.email@company.com",
        "JIRA_API_TOKEN": "your_jira_api_token",
        "JIRA_CUSTOM_HEADERS": "X-Forwarded-User=service-account,X-Company-Service=mcp-atlassian,X-Jira-Client=mcp-integration"
      }
    }
  }
}

Security Considerations:

• Custom header values are masked in debug logs to protect sensitive information
• Ensure custom headers don't conflict with standard HTTP or Atlassian API headers
• Avoid including sensitive authentication tokens in custom headers if already using basic auth or OAuth
• Headers are sent with every API request - verify they don't interfere with API functionality

MCP Atlassian supports multi-cloud OAuth scenarios where each user connects to their own Atlassian cloud instance. This is useful for multi-tenant applications, chatbots, or services where users provide their own OAuth tokens.

Minimal OAuth Configuration:

1. Enable minimal OAuth mode (no client credentials required):

   docker run -e ATLASSIAN_OAUTH_ENABLE=true -p 9000:9000 \
     ghcr.io/sooperset/mcp-atlassian:latest \
     --transport streamable-http --port 9000
   

2. Users provide authentication via HTTP headers:

   • Authorization: Bearer <user_oauth_token>
   • X-Atlassian-Cloud-Id: <user_cloud_id>

Example Integration (Python):

import asyncio
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

user_token = "user-specific-oauth-token"
user_cloud_id = "user-specific-cloud-id"

async def main():
    # Connect to streamable HTTP server with custom headers
    async with streamablehttp_client(
        "http://localhost:9000/mcp",
        headers={
            "Authorization": f"Bearer {user_token}",
            "X-Atlassian-Cloud-Id": user_cloud_id
        }
    ) as (read_stream, write_stream, _):
        # Create a session using the client streams
        async with ClientSession(read_stream, write_stream) as session:
            # Initialize the connection
            await session.initialize()

            # Example: Get a Jira issue
            result = await session.call_tool(
                "jira_get_issue",
                {"issue_key": "PROJ-123"}
            )
            print(result)

asyncio.run(main())

Configuration Notes:

• Each request can use a different cloud instance via the X-Atlassian-Cloud-Id header
• User tokens are isolated per request - no cross-tenant data leakage
• Falls back to global ATLASSIAN_OAUTH_CLOUD_ID if header not provided
• Compatible with standard OAuth 2.0 bearer token authentication

For Confluence Cloud only:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "CONFLUENCE_URL",
        "-e", "CONFLUENCE_USERNAME",
        "-e", "CONFLUENCE_API_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "CONFLUENCE_USERNAME": "your.email@company.com",
        "CONFLUENCE_API_TOKEN": "your_api_token"
      }
    }
  }
}

For Confluence Server/DC, use:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "CONFLUENCE_URL",
        "-e", "CONFLUENCE_PERSONAL_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "CONFLUENCE_URL": "https://confluence.your-company.com",
        "CONFLUENCE_PERSONAL_TOKEN": "your_personal_token"
      }
    }
  }
}

For Jira Cloud only:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "JIRA_URL",
        "-e", "JIRA_USERNAME",
        "-e", "JIRA_API_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "JIRA_URL": "https://your-company.atlassian.net",
        "JIRA_USERNAME": "your.email@company.com",
        "JIRA_API_TOKEN": "your_api_token"
      }
    }
  }
}

For Jira Server/DC, use:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "JIRA_URL",
        "-e", "JIRA_PERSONAL_TOKEN",
        "ghcr.io/sooperset/mcp-atlassian:latest"
      ],
      "env": {
        "JIRA_URL": "https://jira.your-company.com",
        "JIRA_PERSONAL_TOKEN": "your_personal_token"
      }
    }
  }
}

👥 HTTP Transport Configuration

Instead of using stdio, you can run the server as a persistent HTTP service using either:

• sse (Server-Sent Events) transport at /sse endpoint
• streamable-http transport at /mcp endpoint

Both transport types support single-user and multi-user authentication:

Authentication Options:

• Single-User: Use server-level authentication configured via environment variables
• Multi-User: Each user provides their own authentication:
  • Cloud: OAuth 2.0 Bearer tokens
  • Server/Data Center: Personal Access Tokens (PATs)

1. Start the server with your chosen transport:

   # For SSE transport
   docker run --rm -p 9000:9000 \
     --env-file /path/to/your/.env \
     ghcr.io/sooperset/mcp-atlassian:latest \
     --transport sse --port 9000 -vv
   
   # OR for streamable-http transport
   docker run --rm -p 9000:9000 \
     --env-file /path/to/your/.env \
     ghcr.io/sooperset/mcp-atlassian:latest \
     --transport streamable-http --port 9000 -vv
   

2. Configure your IDE (single-user example):

   SSE Transport Example:

   {
     "mcpServers": {
       "mcp-atlassian-http": {
         "url": "http://localhost:9000/sse"
       }
     }
   }
   

   Streamable-HTTP Transport Example:

   {
     "mcpServers": {
       "mcp-atlassian-service": {
         "url": "http://localhost:9000/mcp"
       }
     }
   }
   

Here's a complete example of setting up multi-user authentication with streamable-HTTP transport:

1. First, run the OAuth setup wizard to configure the server's OAuth credentials:

   docker run --rm -i \
     -p 8080:8080 \
     -v "${HOME}/.mcp-atlassian:/home/app/.mcp-atlassian" \
     ghcr.io/sooperset/mcp-atlassian:latest --oauth-setup -v
   

2. Start the server with streamable-HTTP transport:

   docker run --rm -p 9000:9000 \
     --env-file /path/to/your/.env \
     ghcr.io/sooperset/mcp-atlassian:latest \
     --transport streamable-http --port 9000 -vv
   

3. Configure your IDE's MCP settings:

Choose the appropriate Authorization method for your Atlassian deployment:

• Cloud (OAuth 2.0): Use this if your organization is on Atlassian Cloud and you have an OAuth access token for each user.
• Server/Data Center (PAT): Use this if you are on Atlassian Server or Data Center and each user has a Personal Access Token (PAT).

Cloud (OAuth 2.0) Example:

{
  "mcpServers": {
    "mcp-atlassian-service": {
      "url": "http://localhost:9000/mcp",
      "headers": {
        "Authorization": "Bearer <USER_OAUTH_ACCESS_TOKEN>"
      }
    }
  }
}

Server/Data Center (PAT) Example:

{
  "mcpServers": {
    "mcp-atlassian-service": {
      "url": "http://localhost:9000/mcp",
      "headers": {
        "Authorization": "Token <USER_PERSONAL_ACCESS_TOKEN>"
      }
    }
  }
}

4. Required environment variables in .env:

   JIRA_URL=https://your-company.atlassian.net
   CONFLUENCE_URL=https://your-company.atlassian.net/wiki
   ATLASSIAN_OAUTH_CLIENT_ID=your_oauth_app_client_id
   ATLASSIAN_OAUTH_CLIENT_SECRET=your_oauth_app_client_secret
   ATLASSIAN_OAUTH_REDIRECT_URI=http://localhost:8080/callback
   ATLASSIAN_OAUTH_SCOPE=read:jira-work write:jira-work read:confluence-content.all write:confluence-content offline_access
   ATLASSIAN_OAUTH_CLOUD_ID=your_cloud_id_from_setup_wizard
   

[!NOTE]

• The server should have its own fallback authentication configured (e.g., via environment variables for API token, PAT, or its own OAuth setup using --oauth-setup). This is used if a request doesn't include user-specific authentication.
• OAuth: Each user needs their own OAuth access token from your Atlassian OAuth app.
• PAT: Each user provides their own Personal Access Token.
• Multi-Cloud: For OAuth users, optionally include X-Atlassian-Cloud-Id header to specify which Atlassian cloud instance to use
• The server will use the user's token for API calls when provided, falling back to server auth if not
• User tokens should have appropriate scopes for their needed operations

Tools

Key Tools

Jira Tools

• jira_get_issue: Get details of a specific issue
• jira_search: Search issues using JQL
• jira_create_issue: Create a new issue
• jira_update_issue: Update an existing issue
• jira_transition_issue: Transition an issue to a new status
• jira_add_comment: Add a comment to an issue

Confluence Tools

• confluence_search: Search Confluence content using CQL
• confluence_get_page: Get content of a specific page
• confluence_create_page: Create a new page
• confluence_update_page: Update an existing page

Operation	Jira Tools	Confluence Tools
Read	jira_search	confluence_search
	jira_get_issue	confluence_get_page
	jira_get_all_projects	confluence_get_page_children
	jira_get_project_issues	confluence_get_comments
	jira_get_worklog	confluence_get_labels
	jira_get_transitions	confluence_search_user
	jira_search_fields
	jira_get_agile_boards
	jira_get_board_issues
	jira_get_sprints_from_board
	jira_get_sprint_issues
	jira_get_issue_link_types
	jira_batch_get_changelogs*
	jira_get_user_profile
	jira_download_attachments
	jira_get_project_versions
Write	jira_create_issue	confluence_create_page
	jira_update_issue	confluence_update_page
	jira_delete_issue	confluence_delete_page
	jira_batch_create_issues	confluence_add_label
	jira_add_comment	confluence_add_comment
	jira_transition_issue
	jira_add_worklog
	jira_link_to_epic
	jira_create_sprint
	jira_update_sprint
	jira_create_issue_link
	jira_remove_issue_link
	jira_create_version
	jira_batch_create_versions

*Tool only available on Jira Cloud

Tool Filtering and Access Control

The server provides two ways to control tool access:

1. Tool Filtering: Use --enabled-tools flag or ENABLED_TOOLS environment variable to specify which tools should be available:

   # Via environment variable
   ENABLED_TOOLS="confluence_search,jira_get_issue,jira_search"
   
   # Or via command line flag
   docker run ... --enabled-tools "confluence_search,jira_get_issue,jira_search" ...
   

2. Read/Write Control: Tools are categorized as read or write operations. When READ_ONLY_MODE is enabled, only read operations are available regardless of ENABLED_TOOLS setting.

Troubleshooting & Debugging

Common Issues

• Authentication Failures:
  • For Cloud: Check your API tokens (not your account password)
  • For Server/Data Center: Verify your personal access token is valid and not expired
  • For older Confluence servers: Some older versions require basic authentication with CONFLUENCE_USERNAME and CONFLUENCE_API_TOKEN (where token is your password)
• SSL Certificate Issues: If using Server/Data Center and encounter SSL errors, set CONFLUENCE_SSL_VERIFY=false or JIRA_SSL_VERIFY=false
• Permission Errors: Ensure your Atlassian account has sufficient permissions to access the spaces/projects
• Custom Headers Issues: See the "Debugging Custom Headers" section below to analyze and resolve issues with custom headers

Debugging Custom Headers

To verify custom headers are being applied correctly:

1. Enable Debug Logging: Set MCP_VERY_VERBOSE=true to see detailed request logs

   # In your .env file or environment
   MCP_VERY_VERBOSE=true
   MCP_LOGGING_STDOUT=true
   

2. Check Header Parsing: Custom headers appear in logs with masked values for security:

   DEBUG Custom headers applied: {'X-Forwarded-User': '***', 'X-ALB-Token': '***'}
   

3. Verify Service-Specific Headers: Check logs to confirm the right headers are being used:

   DEBUG Jira request headers: service-specific headers applied
   DEBUG Confluence request headers: service-specific headers applied
   

4. Test Header Format: Ensure your header string format is correct:

   # Correct format
   JIRA_CUSTOM_HEADERS=X-Custom=value1,X-Other=value2
   CONFLUENCE_CUSTOM_HEADERS=X-Custom=value1,X-Other=value2
   
   # Incorrect formats (will be ignored)
   JIRA_CUSTOM_HEADERS="X-Custom=value1,X-Other=value2"  # Extra quotes
   JIRA_CUSTOM_HEADERS=X-Custom: value1,X-Other: value2  # Colon instead of equals
   JIRA_CUSTOM_HEADERS=X-Custom = value1               # Spaces around equals
   

Security Note: Header values containing sensitive information (tokens, passwords) are automatically masked in logs to prevent accidental exposure.

Debugging Tools

# Using MCP Inspector for testing
npx @modelcontextprotocol/inspector uvx mcp-atlassian ...

# For local development version
npx @modelcontextprotocol/inspector uv --directory /path/to/your/mcp-atlassian run mcp-atlassian ...

# View logs
# macOS
tail -n 20 -f ~/Library/Logs/Claude/mcp*.log
# Windows
type %APPDATA%\Claude\logs\mcp*.log | more

Security

• Never share API tokens
• Keep .env files secure and private
• See SECURITY.md for best practices

Contributing

We welcome contributions to MCP Atlassian! If you'd like to contribute:

1. Check out our CONTRIBUTING.md guide for detailed development setup instructions.
2. Make changes and submit a pull request.

We use pre-commit hooks for code quality and follow semantic versioning for releases.

License

Licensed under MIT - see LICENSE file. This is not an official Atlassian product.