>>105153600>>105153623>>105153948Kryptonite comes from the shattered remains of Krypton itself, and thus only affects Kryptonians that came from that specific version of Krrpton. Prime is immune because he technically comes from a universe without a Krypton (he's literally a basement dwelling nerd from our world that somehow wound up with Supes' powerset), so no form of kryptonite affects him. Same with magic (he once said a magic attack "tickled").
The only weakness Prime has is red sunlight, since it takes away his powers. There was even one fight with the Legion where that era's Green Lantern had his ring pretty much tell him to run, because there was no red sun within any conceivable distance to bring Prime to. And considering Prime still has Golden Age Superman's powers (read: can literally sneeze an entire solar system away), running was pretty much the only option