After not racing since December 2008, he came back on July 31, 2009, to win the Wickerr Stakes at one mile over the infield Jimmy Durante Turf Course at Del Mar Racetrack ridden by Garrett Gomez. He then ran 5th in the Pacific Classic Stakes to the upset winner Richard's Kid. He also was entered in the Goodwood Stakes and ran second by a neck to Gitano Hernado. Colonel John closed out his career in the 2009 Breeders' Cup Classic by running 5th to Zenyatta.
