For every request to MCP Cursor asks me to confirm run, though I clicked "Allow list MCP"

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Hi Eugen!

This is a known issue that our team is actively investigating. A few things to help narrow down which variant you’re hitting:

  1. When the prompt shows up after you’ve clicked “Allowlist MCP Tool”, does the Jira tool actually still run in the background (you see results come back), or does it genuinely wait until you click “Run”?

  2. In Cursor Settings > Features > Auto-run, which mode is currently selected? (“Use Allowlist”, “Run Everything”, or disabled?)

Workaround in the meantime: You can switch to Cursor Settings > Features > Auto-run and select the mode that bypasses the allowlist prompt entirely for MCP tools. This will auto-approve all tool calls without requiring per-tool allowlisting.

You may also find this related thread helpful, where other users reported the same behavior.