In the 2009 MLB season, Hoffpauir was a PH due to Lee's struggles at first and through April 15 had success with 2 hits in 4 at-bats with 2 RBIs. He also played right field due to the absence of Milton Bradley, hitting his first home run of the season on April 21 at home against the Cincinnati Reds. As a regular, he was hitting .314 as of May 20. But the very next game, he went 0-4 with four strike outs and went on to hit just .209 the rest of the season for a .239 season average. Hoffpauir started 2010 with the AAA Iowa Cubs. In August 2010, he rejoined the Cubs but hit just .173 playing just the final two months of the season.