Following the transfer of Kenny Hill to Texas Christian University, Allen was positioned to be the starter for the Aggies in 2015. On August 24 during the 2015 off-season, Allen was named the starting quarterback against Arizona State with competition from incoming freshman Kyler Murray.
Against Alabama, Allen said he suffered an AC sprain in his throwing shoulder but told the coaching staff he was well enough to face Ole Miss. Allen would then miss playing in the 35–28 win on Oct 31 against South Carolina and the Aggies loss to Auburn (26–10). Murray would start in both of those games and a home win over Western Carolina. Allen would return as the starter on Nov 21, a 25–0 win over Vanderbilt. He played his last game with the Aggies on November 28, 2015, completing 15/28 passes for 161-yards and a touchdown in a 7–19 loss to LSU. He finished his second year with completing 160/283 passes for 2,210-yards, 17 touchdowns, and 7 interceptions. Allen also ran for 65 yards and 2 touchdowns.
On December 10, 2015, Allen announced he would be transferring from Texas A&M. This decision made him unavailable to play in the Aggies' Music City bowl game. Allen ended his Aggies career with 278 completions in 475 attempts (58.5%), 3,532 passing yards, 33 passing touchdowns, and 14 interceptions in 20 games.