MCP Atlassian

Model Context Protocol (MCP) server for Atlassian products (Confluence, Jira, Bitbucket, and Xray for Jira). This integration supports Confluence, Jira, and Bitbucket for both Cloud and Server/Data Center deployments. Xray for Jira is available only on Server/Data Center deployments and always uses the Jira URL and credentials you configure. Note: This project is a fork from mcp-atlassian. The project at the time of making a fork has not been maintained for a while with couple of dozen pull requests and a few issues on the github project. Hence, it was about time to fork the project and make some fixes.

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"

• 🧪 Test Management with Xray for Jira - "Get test execution results for the latest sprint"

• 📊 Quality Assurance Tracking - "Update test run status and add defects found during testing"

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

Related MCP server: MCP Atlassian

Quick Start Guide

🔐 1. Authentication Setup

MCP Atlassian supports four 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

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/SharkyND/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

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.

D. Dynamic Header-Based Authentication - Multi-Tenant

With header-based authentication, you can pass Jira, Confluence, and Bitbucket credentials directly through HTTP headers on each request. Xray for Jira automatically reuses the Jira headers. This method supports both Personal Access Tokens (PAT) for Server/Data Center and API tokens for Cloud deployments.

Required Headers:

For Jira authentication:

• X-Atlassian-Jira-Personal-Token: Your Jira PAT or API token

• X-Atlassian-Jira-Url: Your Jira instance URL

For Confluence authentication:

• X-Atlassian-Confluence-Personal-Token: Your Confluence PAT or API token

• X-Atlassian-Confluence-Url: Your Confluence instance URL

For Bitbucket authentication:

• X-Atlassian-Bitbucket-Personal-Token: Your Bitbucket PAT or app password

• X-Atlassian-Bitbucket-Url: Your Bitbucket instance URL

For Xray for Jira authentication:

• Reuses your Jira headers (X-Atlassian-Jira-Personal-Token and X-Atlassian-Jira-Url), which must point to a Server/Data Center Jira with Xray installed.

• Xray for Jira tools are disabled by default. To enable Xray for Jira tools, set the X-Atlassian-Enable-Xray header to true.

Benefits:

• ✅ No environment variables required

• ✅ Per-request authentication

• ✅ Multi-tenant support

• ✅ Dynamic credential management

• ✅ Zero server configuration needed

• ✅ Works with both Cloud and Server/Data Center

Example MCP Client Configuration:

{
  "Atlassian": {
    "url": "http://localhost:8000/mcp",
    "headers": {
      "X-Atlassian-Jira-Personal-Token": "your_jira_pat_or_api_token",
      "X-Atlassian-Jira-Url": "https://your-jira-instance.com",
      "X-Atlassian-Confluence-Personal-Token": "your_confluence_pat_or_api_token",
      "X-Atlassian-Confluence-Url": "https://your-confluence-instance.com",
      "X-Atlassian-Bitbucket-Personal-Token": "your_bitbucket_pat_or_app_password",
      "X-Atlassian-Bitbucket-Url": "https://your-bitbucket-instance.com",
      "X-Atlassian-Read-Only-Mode": "true",
      "X-Atlassian-Jira-Read-Only-Mode": "false"
    },
    "type": "http"
  }
}

📦 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/SharkyND/mcp-atlassian:latest

🛠️ IDE Integration

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

⚙️ Configuration Methods

There are three 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)

3. Header-Based Authentication (no environment variables required - see Header-Based Authentication Configuration)

📝 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",
        "-e", "BITBUCKET_URL",
        "-e", "BITBUCKET_USERNAME",
        "-e", "BITBUCKET_APP_PASSWORD",
        "ghcr.io/SharkyND/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",
        "BITBUCKET_URL": "https://bitbucket.org",
        "BITBUCKET_USERNAME": "your.email@company.com",
        "BITBUCKET_APP_PASSWORD": "your_bitbucket_app_password"
      }
    }
  }
}

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

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/SharkyND/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"
      }
    }
  }
}

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/SharkyND/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"
      }
    }
  }
}

This configuration uses the new dynamic header-based authentication feature. No environment variables are required - credentials are passed through HTTP headers on each request.

Minimal Docker Configuration (No Environment Variables Needed):

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "ghcr.io/SharkyND/mcp-atlassian:latest"
      ]
    }
  }
}

MCP Client Configuration with Headers:

Configure your MCP client to send authentication headers with each request:

{
  "Atlassian": {
    "url": "http://localhost:8000/mcp",
    "headers": {
      "X-Atlassian-Read-Only-Mode": "true",
      "X-Atlassian-Jira-Read-Only-Mode": "false",
      "X-Atlassian-Jira-Personal-Token": "your_jira_pat_or_api_token",
      "X-Atlassian-Jira-Url": "https://your-jira-instance.com",
      "X-Atlassian-Confluence-Personal-Token": "your_confluence_pat_or_api_token",
      "X-Atlassian-Confluence-Url": "https://your-confluence-instance.com"
    },
    "type": "http"
  }
}

Optional Docker Configuration with Read-Only Mode:

If you want to enable read-only mode globally (rather than per-request), you can still use environment variables:

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "docker",
      "args": [
        "run",
        "--rm",
        "-i",
        "-e", "READ_ONLY_MODE",
        "ghcr.io/SharkyND/mcp-atlassian:latest"
      ],
      "env": {
        "READ_ONLY_MODE": "true"
      }
    }
  }
}

• 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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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/SharkyND/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

Monitoring

Username Requirement

Enforce username headers in requests by setting REQUIRE_USERNAME=true only for monitoring purpose. When the enviroment variable is passed in as true, it will be enable prometheus client to caputre username from the header and avalible to scrape through the service monitor:

# Environment variable
REQUIRE_USERNAME=true

# Helm chart
env:
  REQUIRE_USERNAME: "true"

When enabled, requests must include at least one username header:

• X-Atlassian-Username

Returns 400 error if missing when enabled.

Monitoring & Metrics

Prometheus Metrics available at /metrics endpoint:

• Request counts, duration, errors by service

• User activity tracking (when username headers provided)

• Pod-specific metrics for Kubernetes deployments

Health Checks:

• /healthz - Basic health status

• /readyz - Kubernetes readiness probe

Kubernetes Integration:

• Helm chart with monitoring configuration

• Grafana dashboard provisioning via ConfigMaps

• ServiceMonitor for Prometheus Operator

Read-Only Mode

Read-only mode removes all tools tagged with write from tool discovery and blocks direct calls to write handlers. Unless configured, the server runs in read/write mode.

Read-only mode can be controlled globally (all products) or per-product (Jira, Confluence, Bitbucket independently). The effective state is recalculated on every request using this priority (highest first):

Truthy values: true, 1, yes, on. Falsy values: false, 0, no, off. A falsy value at a higher priority overrides a truthy value at a lower priority.

When enabled for a product, its write tools are hidden in tools/list, and the @check_write_access decorator raises ValueError if a client tries to invoke one directly.

CLI flags

# All products read-only
uv run mcp-atlassian --transport streamable-http --port 8889 --read-only

# Per-product: only Jira is read-only
uv run mcp-atlassian --transport streamable-http --port 8889 --jira-read-only

# Combined: Jira and Confluence read-only, Bitbucket stays read/write
uv run mcp-atlassian --transport streamable-http --port 8889 --jira-read-only --confluence-read-only

Environment variables

# Global — all products
set READ_ONLY_MODE=true               # Windows CMD
$Env:READ_ONLY_MODE = "true"          # PowerShell
export READ_ONLY_MODE=true            # macOS/Linux

# Per-product overrides
$Env:JIRA_READ_ONLY_MODE = "true"      # Jira only
$Env:CONFLUENCE_READ_ONLY_MODE = "true" # Confluence only
$Env:BITBUCKET_READ_ONLY_MODE = "true" # Bitbucket only

# Example: global read-only, but Jira stays read/write
$Env:READ_ONLY_MODE = "true"
$Env:JIRA_READ_ONLY_MODE = "false"

HTTP headers (per-request)

Headers let you override the server defaults on a per-request basis without restarting.

{
  "headers": {
    "X-Atlassian-Read-Only-Mode": "true",
    "X-Atlassian-Jira-Read-Only-Mode": "false",
    "X-Atlassian-Confluence-Read-Only-Mode": "true",
    "X-Atlassian-Bitbucket-Read-Only-Mode": "false"
  }
}

A per-product header always takes precedence over the global header for that product. In the example above, the global flag enables read-only for all products, but the Jira and Bitbucket headers override it back to read/write.

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

Bitbucket Tools

• list_workspaces_or_projects: List all accessible workspaces/projects

• list_repositories: List repositories in a workspace or all accessible repositories

• get_repository_info: Get detailed information about a specific repository

• list_branches: List all branches in a repository

• get_default_branch: Get the default branch of a repository

• get_file_content: Get content of a specific file from a repository

• list_directory: List contents of a directory in a repository

• list_pull_requests: List pull requests for a repository

• pull_request_activities: Get activities/comments for a pull request

• get_pull_request: Get detailed information about a specific pull request

• get_commit_changes: Get changes made in a specific commit

• get_commits: Get commit history for a repository

• create_pull_request: Create a new pull request

• create_branch: Create a new branch in a repository

• add_pull_request_blocker_comment: Add a blocking comment to a pull request

• add_pull_request_comment: Add a regular comment to a pull request

• add_pull_request_inline_comment: Add an inline comment on a specific line of a file in a pull request

Xray Tools

• get_tests: Retrieve information about specific tests

• get_test_statuses: Get all available test statuses

• get_test_runs: Get test runs for a specific test

• get_test_executions: Get test executions for a test

• get_test_plans: Get test plans associated with a test

• create_test_step: Create a new test step for a test

• update_test_step: Update an existing test step

• update_test_run_status: Update the status of a test run

• update_test_run_defects: Associate defects with a test run

*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.