Allen sprained his left ankle in the second quarter against the Tennessee Titans on September 15. He attempted to return in the second half but lasted just two plays before returning to the sideline. He was inactive at Philadelphia on September 22, due to his ankle injury. He moved to right tackle during practice the week leading up to St. Louis Rams game on September 29, and opened the game at that position before re-aggravating his sprained left ankle. He then left the game in the first quarter. He returned to the starting lineup at right tackle against the New York Giants on October 6, but came out during first drive after aggravating left ankle. He fought the pain and was in and out of the game in the second half at left guard for Kelvin Garmon who suffered a hip injury. Following the trade of Garmon to the Chargers, Allen returned to left guard against the Panthers on October 13, but left the game in the second quarter with an ankle pain. He was then inactive next the three games to let the injury heal. He returned to practice the week against the Colts on November 17 but was inactive for a fourth straight game. He was placed on injured reserve on November 21, and underwent successful surgery on December 3, to remove bone spurs from left ankle.