 In addition, he installed and implemented a system of individual player plans which provided instruction and resources to insure the individual development of every Pirate player.Under Graham, the Pirates minor league teams finished with a combined winning percentage above .500 in four of his five seasons.In 2002, the Pirates were honored as the Topps' Baseball “Organization of the Year.”

On September 7, 2007, he was appointed interim General Manager of the Pirates after the dismissal of Dave Littlefield.