EDIT: You also need to set the executablePath setting to explicitly point to juliaup, e.g. "julia.executablePath": "/Users/fred/.juliaup/bin/julia",
As of Dec 2024, there’s a much easier way to do this. Simply run juliaup override set 1.9 in your directory and then the julia command will use version 1.9 when run from that directory, regardless of how you start julia.