Peña signed a minor league contract with the Tampa Bay Devil Rays on February 1, 2007 with an invitation to spring training. The Rays reassigned Peña to minor league camp. With a knee injury to Greg Norton on the last day of spring training, the Rays re-signed him, this time to a Major League contract on April 1.
Peña would go on to have the best season of his career in 2007 and set numerous career highs. He finished the season with a .282 batting average, 46 home runs and 121 RBIs. His batting average, home runs, and RBIs were career highs, as well as games played (148), at bats (490), runs scored (99), doubles (29), total bases (307), on-base percentage (.411), slugging percentage (.627), walks (103), and strikeouts (142). He was second in the American League in home runs to Alex Rodriguez' 54. His home run, RBIs, slugging percentage, on-base percentage and walk totals also set Rays franchise records. In 2007, he had the lowest range factor of all AL league first basemen, 8.73. Peña's season led to his being named the 2007 American League Comeback Player of the Year and he was considered as an AL MVP candidate. He also was named the Player's Choice AL Comeback Player of the Year by fellow players. Peña was allowed to donate $20,000 to Dominican youth under the poverty line.