MCP/Atlassian/Q/Can Atlassian authentication be system wide and cached

• Can Atlassian MCP authentication be system wide and cached?

  • When signing in to Atlassian MCP in Cursor via OAuth in the browser, the authentication does not persist to other tools like Claude/Code or cursor-agent CLI.

  • Answer

    • Short answer: Yes, but only if all tools use mcp-remote with identical configurations. Otherwise, each tool requires separate authentication.

    • How mcp-remote stores credentials

      • mcp-remote stores OAuth tokens in ~/.mcp-auth (or $MCP_REMOTE_CONFIG_DIR)
      • Tokens are keyed by a hash of the server URL + resource flag + custom headers
      • If two tools invoke mcp-remote with the exact same arguments, they share the cached token

    • Why authentication doesn't persist across tools

      • Different tools store MCP configurations differently:
        • Cursor: ~/.cursor/mcp.json
        • Claude Code: ~/.claude.json (via claude mcp add)
        • Claude Desktop: ~/Library/Application Support/Claude/claude_desktop_config.json
      • If the command arguments differ at all (even whitespace or argument order), mcp-remote generates a different hash → separate OAuth session

    • Solutions

      • Option 1: Ensure identical mcp-remote invocations

        • Configure each tool to use the exact same command:
        • json

          {
            "command": "npx",
            "args": ["-y", "mcp-remote", "https://mcp.atlassian.com/v1/sse"]
          }

        • Once authenticated in one tool, other tools with identical config will reuse ~/.mcp-auth tokens

      • Option 2: Use self-hosted mcp-atlassian with API tokens

        • The unofficial mcp-atlassian server supports API token authentication
        • Store your Atlassian API token in environment variables or 1Password
        • No OAuth flow required — works identically across all tools
        • See mcp-atlassian/How To/Install with 1Password Creds

      • Option 3: Re-authenticate in each tool

        • Run /mcp in Claude Code and authenticate separately
        • Each tool maintains its own OAuth session
        • Tokens refresh automatically within each tool

    • Current limitations

      • The official Atlassian/MCP server (Rovo MCP) requires OAuth 2.1 — API keys and OIDC are not supported
      • There is no central system-wide OAuth token store that all MCP clients share by design
      • mcp-remote is the closest to system-wide caching, but requires configuration consistency

  • My Notes

    • The root issue is that MCP client tools (Cursor, Claude Code, etc.) each have their own configuration systems and don't coordinate on how they invoke mcp-remote
    • A potential improvement would be for mcp-remote to normalize configurations before hashing, or for tools to adopt a shared MCP configuration standard

  • Related

    • MCP/Atlassian/Reference/Authentication API Key vs OAuth
    • Atlassian/MCP/How To/Set up in Cursor
    • mcp-atlassian
    • mcp-remote
    • Claude/Code/Tutorial/Connect to MCP Servers