Cooper was appointed manager of League Two Notts County on 20 March 2016 on a short-term contract until the end of the season. He was set a points target which, if met, would bring a permanent deal. He met the target, but left the club to become manager of Forest Green Rovers; when he joined, on 9 May, they had just reached the 2016 National League play-off Final, although caretaker manager Scott Bartlett took charge for the final at Wembley with Cooper in an advisory role.