Allen spent three seasons as the linebackers coach and special teams coordinator at Ole Miss under head coach Hugh Freeze. During his time in Oxford, the Rebels went 24–15 and consistently ranked near the top of the FBS in terms of tackles for loss and sacks. Prior to his arrival, Ole Miss had ranked last in the SEC in total defense.
In December 2014, Allen was named defensive coordinator at South Florida under third-year head coach Willie Taggart. In his lone season in Tampa, Allen's defensive unit ranked first the American Athletic Conference (AAC) in scoring defense at just 19.6 points per conference game.
Allen was hired on January 15, 2016 to serve as defensive coordinator on head coach Kevin Wilson's staff at Indiana. In replacing previous defensive coordinator Brian Knorr, Allen took over a defense that ranked #120 in the FBS in total defense and #106 in opponent points scored. As of December 1, 2016, the Hoosiers' defense ranks #35 in the FBS in total defense (8th best in the Big Ten) and #53 in opponent points scored.
On December 1, 2016, Indiana athletic director Fred Glass named Allen head coach after Wilson's sudden resignation.