"He is a teacher in my college."
他是我大学的老师: "He is a teacher at/in my college"
Your translation, 他在我的大学(里)是老师 sounds a bit off. As in it's not the normal way people would talk. It sounds like an answer to the theoretical question "What is his position at your college"
Alternatively, you could use 当 instead of 是, where the former means something among the lines of "to be in the position of (CEO, teacher, etc. for example)"
edit: Neither of your sentences is wrong per se, in the end it just comes down to small subtleties