What it means
A cheer to leave someone alone while they are clearly onto something good, like a chef mid-recipe. When a mate is on a roll, ranting brilliantly or building something clever, you let them cook, no interrupting, no doubting, just trust the process and watch.
Usage examples
"He has not said why yet but his plan always works out, let him cook."
"Stop questioning her, she knows what she is doing, let her cook."
"Nah, don't cut him off yet, let them cook, this story's about to land."
"Everyone was clowning the idea at first, then we stepped back and let them cook."
Where it comes from
This comes from the older call let him cook, which blew up in sports talk, gaming chat, and meme culture in the late 2010s and early 2020s. The kitchen bit is the whole joke: if someone's cooking, they're in their bag, building something good, so you don't mess with the process.