On 4 July 2011, Margetson quit his coaching job at Cardiff in order to join up with Sam Allardyce at West Ham United as their new goalkeeping coach. In October 2014, following the appointment of new Cardiff manager, Russell Slade, Margetson returned as goalkeeping coach to Cardiff City. In August 2016, Margetson stepped down from his role with Wales to join the England national football team coaching staff, following the appointment of Sam Allardyce. On 12 January 2017 it was announced that Margetson had joined Crystal Palace as goalkeeping coach. He joined Everton in December 2017, and left on 16 May 2018 after the departure of Sam Allardyce.