Pena was acquired by the Red Sox back in 2006 in exchange for Bronson Arroyo and cash. In 2006, Pena hit .301 with 11 home runs and 42 RBI in 84 games. The next season, Pena's numbers dipped, as the young slugger only managed a .218 batting average with five home runs and 17 RBI in 73 games with Boston.
On August 17, 2007, Pena was traded to the Washington Nationals for a player to be named later (Chris Carter). Pena went on to hit ..293 with eight home runs and 22 RBI in 37 games with the Nationals that season.
Up until now, Pena has been playing in the D'Backs organization in the Pacific Coast League, where he has been on a tear, batting .363 with 21 home runs and 63 RBI through 29 games this season.