In 1929, leaving the CB&Q again (to be succeeded by Frederick E. Williamson), Holden became chairman of the executive committee for Southern Pacific Railroad (succeeding Henry deForest); he was promoted to chairman of the Southern Pacific in 1932, and finally retired in 1939. Since the Southern Pacific management team was based in New York, Holden also maintained an apartment there at 610 Park Avenue in addition to his home in Chicago.
