Beilein's first Division I head coaching position was at Canisius, a hometown school of which he had been a fan. He turned around the school's losing program and helped it earn two National Invitation Tournament (NIT) bids and one NCAA Tournament appearance in five years. Next, at Richmond, he reached the NCAA Tournament once and NIT twice in five years. He moved on to West Virginia, where his teams reached the second weekend of the NCAA Tournament twice, and also twice went to the NIT, including one championship. At Michigan, where he became the school's winningest coach, he won two Big Ten regular-season championships, two Big Ten Tournament titles, and in the NCAA Tournament twice advanced as far as the national championship game. He has a 26–13 career record in the NCAA tournament, with championship game appearances in 2013 and 2018, as well as a 13–6 record in the NIT.