Allen joined the Stone Crabs coaching staff in 2010. As the pitching coach, he helped steer the pitching staff to 80 wins while leading the league with a 3.06 ERA and 1189 strikeouts. He has been with the Rays organization since 2007. Prior to that he was a pitching coach split time with the Blue Jays and Yankees organizations since 1998. As a player, Allen was drafted in the 11th round of the 1976 Draft and pitched for 14 seasons with Mets, Cardinals, Yankees, Indians and Reds organizations.
In December of 2010, the Rays announced that Allen would be the pitching coach for AAA Durham Bulls in 2011.