Allen was called up to the majors for the first time on August 22, 2009, and made his debut that day.[2] He finished the game one for four with a single. Allen would play in 32 games that season and finished with a .202 batting average, four home runs, and 14 RBIs.
After spending most of the 2010 season at Triple-A Reno, Allen was called up on September 1, 2010. In his first game against the San Diego Padres, he hit his first career grand slam. He finished the season with a .267 batting average in 22 games.
On August 23, 2011, Allen became only the second player in history to hit a home run into the upper deck at the New Yankee Stadium (Russell Branyan being the first). Later in the game he hit a shorter home run into the second deck to help the Athletics defeat the Yankees 6–5.
On April 9, 2012, Allen was designated for assignment.
Tampa Bay Rays
On April 19, 2012, Allen was claimed off waivers from the Oakland Athletics by the Tampa Bay Rays.
Allen had his first career hit as a member of the Tampa Bay Rays, a two-run walk-off home run against the Los Angeles Angels of Anaheim which resulted in the Rays sweeping the series. He was again designated for assignment and was subsequently released.
Texas Rangers
In 2013, Allen signed a minor league deal with an invitation to spring training by the Rangers. By the end of spring training, Allen was released by the Rangers.
San Diego Padres
On April 9, 2013, Allen signed a minor league deal with the Padres. He played 2013 with Triple-A Tucson, where he was used mostly at first base, but also played in 40 games in left field. In 119 games with the Padres, he hit .267 with 17 HR, 76 RBI and 24 doubles.
New York Mets
On November 19, 2013, Allen signed a minor league deal with the New York Mets. He spent 2014 and 2015 with their AAA affiliate, the Las Vegas 51s.
Cincinnati Reds
On November 30, Allen signed a minor league deal with the Cincinnati Reds.[4] on April 8, 2016, Allen had his contract purchased by the Reds. He was designated for assignment two days later without appearing in a game. He became a free agent on October 11, 2016.