Texas A&M got off to a 5–0 start, as Allen led the SEC in passing efficiency. Then, against Alabama, he threw three interceptions that were returned for touchdowns in a 41–23 loss. During that game, on Oct 16, he had a 50 percent completion rate. He went 12-for-34 passing (35.3 percent passing completion rate) for 88 yards in a 23–3 loss to Ole Miss on Oct. 24. The Friday before the following game, head coach Kevin Sumlin named Kyler Murray the starter and Allen started to practice with the third team.
On September 14, 2014, he made his first appearance with the Aggies and threw 12/16 completions for 122-yards, 2 touchdowns, and an interception. The next week he took on #3 Auburn in Auburn, Alabama. He led the unranked Aggies past the Tigers while throwing for 277 yard and 4 touchdowns along with 1 interception in a 41-38 win, ending Auburn'a chances of making the playoffs and putting A&M back in the Top 25.
On December 10, 2015, Allen announced he would be transferring from Texas A&M and then over two weeks later, the Aggies' other quarterback, Kyler Murray, announced he would be transferring. . 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. It was announced on January 5, 2016, that Kyle Allen intended to transfer to the University of Houston.
Allen began classes at Houston on January 19, 2016, but was not be eligible to play for the Cougars during the 2016 season due to NCAA transfer guidelines that require transfers to sit out a single year.
Through the end of the 2017 season, Allen's statistics are as follows:
Allen then proceed to be benched in favor of Kyle Postma during UH's third game Against Texas Tech after throwing 4 interceptions in 3 games. On January 11, 2018, Allen announced his decision to forgo his senior season and declare for the 2018 NFL Draft.
