On April 1, 2008, Crean was hired as head coach of the Indiana Hoosiers, succeeding interim head coach Dan Dakich. Dakich had replaced former coach Kelvin Sampson, who resigned after NCAA recruiting violations. Between Crean's hiring and the start of the 2008–09 season, freshman Eric Gordon opted to leave early for the NBA and star forward DJ White graduated. Two players kicked off the team by Dakich were not allowed back by Crean, one was dismissed by Crean and two transferred. As a result, Crean began with a roster consisting only of two walk-ons who had scored a combined 36 points in their careers. Despite the long odds, Crean was known to approach games and practices as if Indiana could compete in each one and to continue stressing Hoosier Hysteria and the long tradition of success at the school.[2] He was well aware that he was walking into a difficult situation. However, when asked why he left Marquette, Crean replied, "It's Indiana. It's Indiana, and that is the bottom line."
With a depleted roster and damaged recruiting lure, Crean's first three seasons saw consecutive losing records of 6–25 (the worst in school history), 10-21, and 12-20. However, during this period Crean's recruiting classes progressively improved, most notably with the signing of five-star recruit and McDonald's All-American Cody Zeller, an Indiana native and lifelong Indiana Hoosier fan. Zeller was the highest ranked recruit to join the Indiana program since the Sampson era.