Beilein has never served as an assistant coach; he has held head-coaching positions throughout his career. He served as the coach of Erie Community College from 1978 to 1982, Western New York's Division III Nazareth College in Rochester, New York for the 1982–1983 school year, and Le Moyne College from 1983 to 1992. Le Moyne was a Division II contestant in the Mideast Collegiate Conference (MCC). Beilein first applied to coach Division I basketball at Canisius in 1987, but he was not hired. During his time at Le Moyne, he held annual coaching clinics that welcomed coaches and athletes. Beilein was named the 1988 MCC Coach of the Year, when his team finished as co-conference champions with a 21–5 regular season record and number 14 national ranking. The team tied with Gannon University with an 8–2 conference record. Although it was Beilein's third 20-win team at Le Moyne, they had never gone to the NCAA tournament before. The team captured the conference post-season tournament after receiving a first round bye. As the number three seed, they faced the number one seeded California University of Pennsylvania in the NCAA Division II Eastern Regionals. They lost their first-round game to fall to a 23–6 record, but won the consolation game against Kutztown University of Pennsylvania.