In 1992, Baron began a 20-season stint as a head coach in the Atlantic 10 Conference, returning to St. Bonaventure once again, this time as head coach. During his nine seasons as head coach, St. Bonaventure appeared in the 1995 National Invitation Tournament and 2000 NCAA tournament, the program's first NCAA Tournament appearance since 1978.
Baron's tenure as head coach of St. Bonaventure spanned two decades in the Atlantic 10 Conference, marking a return to his alma mater. During his nine seasons at the helm, St. Bonaventure experienced significant success by participating in the National Invitation Tournament and NCAA tournament, ending a long period without an NCAA Tournament appearance.