[2] As a freshman in 2015, Allen played in all 12 games of the regular season, primarily as a member of the special teams unit.
[2] In 2016, Allen played in 13 games (2016 Quick Lane Bowl), making one start against Georgia Tech in Dublin.
In the 2016 Quick Lane Bowl, Allen played a big part in the victory over the Maryland Terrapins, recording a single-game career high of 2 sacks for a loss of 15 yards, along with 2 solo tackles.
[3] After posting a career-high 14 tackles against Virginia Tech, Allen was named the Atlantic Coast Conference Defensive lineman of the week.
[4] After the season, Allen won the Bulger Love Award, given to New England's best offensive and defensive NCAA football players.
[5] There was speculation that Allen would declare for the 2018 NFL draft after his junior season, but he later announced that he would return to school for his senior year.
[15] In Week 15 against the Philadelphia Eagles, Allen led the team with 11 tackles and sacked Jalen Hurts once during the 33–26 win.