Configuration

IDE integration, environment variables, and advanced configuration options

Configuration

This guide covers IDE integration, environment variables, and advanced configuration options.

IDE Integration

Configuration File Locations

IDE	Location
Claude Desktop (Windows)	%APPDATA%\Claude\claude_desktop_config.json
Claude Desktop (macOS)	~/Library/Application Support/Claude/claude_desktop_config.json
Claude Desktop (Linux)	~/.config/Claude/claude_desktop_config.json
Cursor	Settings → MCP → + Add new global MCP server

Basic Configuration (uvx)

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "uvx",
      "args": ["mcp-atlassian"],
      "env": {
        "JIRA_URL": "https://your-company.atlassian.net",
        "JIRA_USERNAME": "[e-mail]",
        "JIRA_API_TOKEN": "your_api_token"
      }
    }
  }
}

Docker with Environment File

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

Server/Data Center Configuration

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "uvx",
      "args": ["mcp-atlassian"],
      "env": {
        "JIRA_URL": "https://jira.your-company.com",
        "JIRA_PERSONAL_TOKEN": "your_pat",
        "JIRA_SSL_VERIFY": "false",
        "CONFLUENCE_URL": "https://confluence.your-company.com",
        "CONFLUENCE_PERSONAL_TOKEN": "your_pat",
        "CONFLUENCE_SSL_VERIFY": "false"
      }
    }
  }
}

Single Service Configuration

Confluence Only

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "uvx",
      "args": ["mcp-atlassian"],
      "env": {
        "CONFLUENCE_URL": "https://your-company.atlassian.net/wiki",
        "CONFLUENCE_USERNAME": "[e-mail]",
        "CONFLUENCE_API_TOKEN": "your_api_token"
      }
    }
  }
}

Jira Only

{
  "mcpServers": {
    "mcp-atlassian": {
      "command": "uvx",
      "args": ["mcp-atlassian"],
      "env": {
        "JIRA_URL": "https://your-company.atlassian.net",
        "JIRA_USERNAME": "[e-mail]",
        "JIRA_API_TOKEN": "your_api_token"
      }
    }
  }
}

Environment Variables

Connection Settings

Variable	Description
JIRA_URL	Jira instance URL
JIRA_USERNAME	Jira username (email for Cloud)
JIRA_API_TOKEN	Jira API token (Cloud)
JIRA_PERSONAL_TOKEN	Jira Personal Access Token (Server/DC)
JIRA_SSL_VERIFY	SSL verification (true/false)
CONFLUENCE_URL	Confluence instance URL
CONFLUENCE_USERNAME	Confluence username (email for Cloud)
CONFLUENCE_API_TOKEN	Confluence API token (Cloud)
CONFLUENCE_PERSONAL_TOKEN	Confluence Personal Access Token (Server/DC)
CONFLUENCE_SSL_VERIFY	SSL verification (true/false)

Filtering Options

Variable	Description	Example
JIRA_PROJECTS_FILTER	Limit to specific Jira projects	PROJ,DEV,SUPPORT
CONFLUENCE_SPACES_FILTER	Limit to specific Confluence spaces	DEV,TEAM,DOC
ENABLED_TOOLS	Enable only specific tools	confluence_search,jira_get_issue

Server Options

Variable	Description
TRANSPORT	Transport type (stdio, sse, streamable-http)
STATELESS	Enable stateless mode for streamable-http (true/false)
PORT	Port for HTTP transports (default: 8000)
HOST	Host for HTTP transports (default: 0.0.0.0)
READ_ONLY_MODE	Disable write operations (true/false)
MCP_VERBOSE	Enable verbose logging (true/false)
MCP_VERY_VERBOSE	Enable debug logging (true/false)
MCP_LOGGING_STDOUT	Log to stdout instead of stderr (true/false)

See .env.example for all available options.

Proxy Configuration

MCP Atlassian supports routing API requests through HTTP/HTTPS/SOCKS proxies.

Variable	Description
HTTP_PROXY	HTTP proxy URL
HTTPS_PROXY	HTTPS proxy URL
SOCKS_PROXY	SOCKS proxy URL
NO_PROXY	Hosts to bypass proxy
JIRA_HTTPS_PROXY	Jira-specific HTTPS proxy
CONFLUENCE_HTTPS_PROXY	Confluence-specific HTTPS proxy

Service-specific variables override global ones.

Custom HTTP Headers

Add custom HTTP headers to all API requests. Useful in corporate environments.

Variable	Description
JIRA_CUSTOM_HEADERS	Custom headers for Jira requests
CONFLUENCE_CUSTOM_HEADERS	Custom headers for Confluence requests

Format: Comma-separated key=value pairs.

JIRA_CUSTOM_HEADERS=X-Forwarded-User=service-account,X-Custom-Auth=token
CONFLUENCE_CUSTOM_HEADERS=X-Service=mcp-integration,X-ALB-Token=secret

Header values are masked in debug logs for security.

Tool Filtering

Control which tools are available:

# Enable specific tools
ENABLED_TOOLS="confluence_search,jira_get_issue,jira_search"

# Read-only mode (disables all write operations)
READ_ONLY_MODE=true

Command-line alternative:

uvx mcp-atlassian --enabled-tools "confluence_search,jira_get_issue"