After being drafted by the Cubs, Hoffpauir was sent to the Single-A Boise Hawks, where he batted .301 with 10 home runs and 41 runs batted in. His good play caused the Cubs to send him to their other Single-A team, the Daytona Cubs, in . There he batted only .254 with 8 home runs and 58 RBIs. In , Hoffpauir made the leap from Single-A Daytona to Triple-A Iowa, where he played in only one game before being sent down to the Double-A West Tenn Diamond Jaxx. He hit 11 home runs and drove in 75 runs in 94 games with the Diamond Jaxx. In , Hoffpauir began the season with Triple-A Iowa, where hit only 3 home runs and drove in 47 runs in 119 games, and batted .268. His poor performance resulted in him being sent back down to Double-A West Tenn for the remainder of the season. He began the campaign with West Tenn, but was moved up to Triple-A Iowa, where he had his best offensive production year of his career with 22 home runs and 80 RBIs to go along with .267 average. With all-star Derrek Lee at first base on the major league team and no openings in the outfield available, Hoffpauir returned to Triple-A Iowa for the season. On July 4, Hoffpauir was placed on the disabled list with a right knee injury. Hoffpauir went on the DL hitting .316 with 16 home runs and 73 RBIs in 82 games.