Johnson stepped down as head basketball coach after the 1939–40 season. The position passed to a few different coaches before Woody Clements took over from 1944–51 and 1953–55, compiling a record of 113–119 (.487). The Lobos won the Border Conference in 1944 and 1945, and they appeared in the NAIA post-season tournament in 1947, losing to Hamline University in the first round. From 1951–62, the Lobos competed in the Mountain States Conference, known at the time as the Skyline Eight. In 1957, while still on faculty, Johnson oversaw construction of the 7,800-seat arena that bears his name, Johnson Gymnasium. For many years, Johnson Gym was the most prominent feature of the UNM campus for those driving along Central Avenue in Albuquerque, part of historic U.S. Route 66.