Does the university of your undergrad make a difference to your medical school application?
I am in the Nanotechnology Engineering program at the University of Waterloo, which is the best engineering program at the best engineering institution in Canada.

I am planning to take some of my pre-med courses like Biology and Immunology at my University. Would it make a difference if my university is not that well known for undergraduate studies in sciences? Or does my MCAT score compensate for the quality of my university?

Generally they should just check your earned units/subjects and grades. But some medical schools are very particular, they will dig further on the reputation of your undergrad school when it comes to medical related subjects. They value their reputation so much that they don't want have unqualified students. Just do good on oral and written exams to prove to them that you are qualified. Heart Surgery