In May 1948, Minnesota hired Cowles away from Michigan after a snowstorm prevented Minnesota from hiring the now-legendary John Wooden. He coached the Gophers from 1948 through 1959. In his first season at Minnesota, Cowles led the basketball team to an 18–3 record (.857) and a No. 6 ranking in the final AP poll. He compiled a 148-93 record at Minnesota, though "he was never able to find the championship touch that he worked at Dartmouth, Michigan and earlier at Carleton College." Despite the lack of championships, his tenure at Minnesota has been described by some as the "golden age" of the program.