Joe later was a successful college head coach for 33 seasons. He coached at Cheyney University of Pennsylvania from 1972 to 1978, Central State University from 1981 to 1993, Florida A&M University from 1994 to 2004, and Miles College from 2007 to 2010. Joe achieved his greatest success at Central State, where his teams won 2 NAIA National Football Championships in 1990 and 1992 and made many appearances in the NAIA football playoffs during the 1980s and 1990s. He teams at Florida A&M have made various appearances in the Division I-AA (now FCS) playoffs during the 1990s and early 2000s.