In 1935, after retiring as a player, Neun began managing in the New York Yankees' farm system, and from 1938 through 1941, he piloted the AA Newark Bears, winning International League regular season championships in 1938 (104 wins) and 1941 (100 wins) and the 1938 playoff title. He then spent two seasons as skipper of the Yanks' other top affiliate, the Kansas City Blues of the American Association (where he won another regular-season pennant, in 1942), before joining the New York coaching staff in 1944.