MCP Server OAuth (authv2) – Validation failed / Missing PKCE verifier issue

Rovo Dev
1
  1. We have an internal AI application
  2. We want to connect it with Jira Cloud via MCP
  3. Authentication should be OAuth-based (per user login)
    MCP Server URL used:https://mcp.atlassian.com/v1/mcp and https://mcp.atlassian.com/v1/mcp/authv2
  4. We also have an OAuth 2.0 (3LO) app created in Atlassian Developer Console
  5. Validation failed Authentication Failed Missing PKCE verifier in state
    1. Looks like MCP requires OAuth 2.1 with PKCE flow
    2. However, our platform validation seems to be happening server-to-server without a browser redirect
    3. We are unsure:
      • Whether MCP supports integration from custom backend/UI tools
      • Whether we should use our own 3LO OAuth app or MCP-managed OAuth
      • How PKCE state is expected to be handled in such integrations
        1. Can Atlassian MCP Server be used with custom AI/backend applications, or is it only supported with MCP-native clients (like Claude, VS Code, etc.)?
        2. Should we use our own OAuth 2.0 (3LO) app, or is MCP expected to manage OAuth internally?
        3. How should the PKCE flow (code_verifier/state) be handled when the client is not a browser-based MCP client?
        4. Is there any supported pattern or reference implementation for integrating MCP with custom applications?