Mizerock moved to the Philadelphia Phillies organization in as hitting coach of their Florida State League affiliate, the Clearwater Threshers. He became the assistant hitting coach of the Philadelphia Phillies on December 18, 2013, and later became their third base coach. He was not retained by the Phillies following the 2015 season. He later accepted a position as a coach for Philadelphia's Short Season-A team, the Williamsport Crosscutters for the 2016 season. Mizerock was named as the pitching coach for the Clearwater Threshers of the 2018 season.