After the 2003–04 season, head coach Cliff Ellis was fired from Auburn. In the summer of 2004, Killingsworth declared himself eligible for the 2004 NBA draft as an early entrant, but he did not hire an agent and later withdrew his name. Not wanting to play at Auburn without Ellis, Killingsworth decided to transfer to Indiana. He had to sit out the whole 2004–05 season due to NCAA transfer rules, and was eligible again to play his senior year for the 2005–06 season. Killingsworth chose to wear jersey number 5 at Indiana, where he was listed at , up from his playing weight in his junior season at Auburn.