Cannot auto-run MCP tools

[my_username_123]

Hi team,
I am using Cursor 0.48.8 on MacOS Sequoia 15.3.2. I am not able to get auto-run (YOLO) mode to work. In previous versions when there was a prompt allowing us to specify with natural language which commands to run, it would work for me, but now it will not auto-run anything. I have an MCP server configured, and each time it asks us to click “Run Tool” and I don’t see any other option to configure an auto-run. Similarly for simple terminal commands like pytest, whether or not they’re in the command allowlist. But I’d prefer to focus on getting MCP tools to auto-run. Showing some attached screenshots.

^ This confirms I have the mode turned on. I have also tried adding “mcp” and the names of my MCP tools and MCP server to the allowlist. None of the above works. Always looks like this:

Any tips or guidance would be appreciated. Thank you!

[msfeldstein]

Can you update to 49 and tell me if this is still happening

[curlyz]

working, but not sure 49 fix it, I notice there is a MCP tools protection setting enabled. I would suggest to display a small logo on the run tool to help user understand why their tools not auto run