Claude Desktop Configuration¶

Configure Claude Desktop to use the Atlassian MCP Server.

Configuration File Location¶

OS	Path
macOS	`~/Library/Application Support/Claude/claude_desktop_config.json`
Windows	`%APPDATA%\Claude\claude_desktop_config.json`
Linux	`~/.config/Claude/claude_desktop_config.json`

Basic Configuration¶

With Direct Credentials¶

{
  "mcpServers": {
    "atlassian": {
      "command": "/path/to/mcp-atlassian",
      "env": {
        "ATLASSIAN_URL": "https://example.atlassian.net",
        "ATLASSIAN_USERNAME": "user@example.com",
        "ATLASSIAN_API_TOKEN": "your-api-token"
      }
    }
  }
}

With 1Password¶

{
  "mcpServers": {
    "atlassian": {
      "command": "/path/to/mcp-atlassian",
      "env": {
        "ATLASSIAN_URL": "https://example.atlassian.net",
        "OP_SERVICE_ACCOUNT_TOKEN": "ops_...",
        "OMNITOKEN_VAULT_URI": "op://MyVault",
        "OMNITOKEN_CREDENTIALS_NAME": "atlassian"
      }
    }
  }
}

With Bitwarden¶

{
  "mcpServers": {
    "atlassian": {
      "command": "/path/to/mcp-atlassian",
      "env": {
        "ATLASSIAN_URL": "https://example.atlassian.net",
        "BW_ACCESS_TOKEN": "...",
        "BW_ORGANIZATION_ID": "...",
        "OMNITOKEN_VAULT_URI": "bw://org-id",
        "OMNITOKEN_CREDENTIALS_NAME": "atlassian"
      }
    }
  }
}

With Keeper¶

{
  "mcpServers": {
    "atlassian": {
      "command": "/path/to/mcp-atlassian",
      "env": {
        "ATLASSIAN_URL": "https://example.atlassian.net",
        "KSM_TOKEN": "US:...",
        "OMNITOKEN_VAULT_URI": "keeper://",
        "OMNITOKEN_CREDENTIALS_NAME": "atlassian"
      }
    }
  }
}

Environment Variables Reference¶

Variable	Description
`ATLASSIAN_URL`	Atlassian instance URL
`ATLASSIAN_USERNAME`	Atlassian username/email
`ATLASSIAN_API_TOKEN`	Atlassian API token
`OMNITOKEN_VAULT_URI`	Vault URI (e.g., `op://MyVault`)
`OMNITOKEN_CREDENTIALS_NAME`	Credential name in vault (default: `atlassian`)
`OP_SERVICE_ACCOUNT_TOKEN`	1Password service account token
`BW_ACCESS_TOKEN`	Bitwarden access token
`BW_ORGANIZATION_ID`	Bitwarden organization ID
`KSM_TOKEN`	Keeper token (format: `REGION:TOKEN`)

Multiple Servers¶

You can run multiple MCP servers alongside Atlassian:

{
  "mcpServers": {
    "atlassian": {
      "command": "/path/to/mcp-atlassian",
      "env": {
        "ATLASSIAN_URL": "https://example.atlassian.net",
        "ATLASSIAN_USERNAME": "user@example.com",
        "ATLASSIAN_API_TOKEN": "token"
      }
    },
    "google": {
      "command": "/path/to/mcp-google",
      "env": {
        "GOOGLE_CREDENTIALS_FILE": "/path/to/service-account.json"
      }
    },
    "aha": {
      "command": "/path/to/mcp-aha",
      "env": {
        "AHA_DOMAIN": "mycompany",
        "AHA_API_TOKEN": "token"
      }
    }
  }
}

Troubleshooting¶

Server Not Starting¶

Check the Claude Desktop logs:

macOS: ~/Library/Logs/Claude/
Windows: %APPDATA%\Claude\logs\

Common issues:

Binary not found: Verify the path is correct
Credentials not found: Check environment variables
Permission denied: Ensure the binary is executable (chmod +x)
Invalid URL: Check ATLASSIAN_URL format

Verifying Configuration¶

Test the server manually:

# Should start and wait for input (Ctrl+C to exit)
/path/to/mcp-atlassian --base-url https://example.atlassian.net \
                        --username user@example.com \
                        --api-token your-token

JSON Syntax Errors¶

Validate your JSON:

# On macOS/Linux
cat ~/Library/Application\ Support/Claude/claude_desktop_config.json | python3 -m json.tool

Available Tools in Claude¶

Once configured, you can ask Claude to:

"Read Confluence page 12345"
"Search for Confluence pages about authentication"
"Create a new page in TEAM space"
"Update page 12345 with a status table"
"Search for open Jira bugs in project FOO"
"Create a new Story in project PROJ"
"Transition PROJ-123 to Done"
"Show velocity report for board 42"