[2] In 2009, Peña made the Yankees Opening Day roster, beating out Ángel Berroa to be the utility infielder.

On 14 April against the Tampa Bay Rays, Pena started his first career game at third base, going 0 for 3 with a walk.

[4] With the acquisition of Eric Hinske on 29 June 2009, Peña was optioned to the Triple-A Scranton/Wilkes-Barre Yankees of the International League to receive regular at-bats and learn to play in the outfield.

[8] He hit his first major league home run on 28 September 2009, off of Kansas City Royals pitcher Luke Hochevar at Yankee Stadium.

[9] Peña was added to the postseason roster after Melky Cabrera was injured in Game 4 of the 2009 World Series.

[11] He stayed with the big league club all year, but only managed to hit .227/.258/.247, one of the worst offensive seasons in team history.

[19] He was optioned back to Triple-A on 1 August 2012, after the Yankees acquired Casey McGehee from the Pittsburgh Pirates.

[27] Peña signed a minor league deal with the San Diego Padres on 26 January 2015.

On 13 December 2015, Peña signed a minor league deal with the San Francisco Giants.

Peña played in 93 games for the Sultanes in 2019, he hit .349/.384/.540 with 13 home runs, 64 RBI, and six stolen bases.

[37] Peña was selected to play for the Mexico national team in the 2013 World Baseball Classic and 2019 exhibition games against Japan.