After days of speculation, on 13 November 2009, Cooper agreed in principle to a three-and-a-half-year contract to become Darren Ferguson's successor as manager of Championship side Peterborough United. He was appointed as manager the following day. He left Kettering second in the table and on a twelve-game unbeaten run. The Poppies were also in the Second Round of the FA Cup, and had been handed a dream tie against Leeds United. Cooper managed his last game as a Poppy away at Cambridge United where his side won 2–0, Cooper was applauded off the pitch by the Kettering Town faithful and had tears running down his cheeks.