He was appointed as manager of Wimbledon in June 2002 after a successful spell as caretaker. He replaced Terry Burton, who had criticised the club's owners over the proposed move to Milton Keynes. Murdoch led Wimbledon to tenth in the First Division in the 2002–03 season, despite a number of supporters boycotting Wimbledon's matches in protest against the proposed move. At then end of the season, the club was placed into administration and a number of the club's players were sold off.
In July 2005, Murdoch joined Bournemouth as part-time goalkeeping coach. He was appointed joint caretaker manager, with Joe Roach, in September 2006 and held the post until Kevin Bond took over in October. He returned to his original role as goalkeeping coach after this. He moved to Norwich City as goalkeeping coach in January 2008, linking up again with Norwich boss Glenn Roeder. Murdoch left this role after just four days, citing personal reasons. Later that month he linked up with Kenny Jackett, with whom he had worked at Watford, to become chief scout at Milwall.
On 1 August 2009, Southampton announced that Murdoch had been appointed as a part-time goalkeeping coach and scout, but he was "relieved of his duties" along with Alan Pardew on 30 August 2010. He took up a similar role at Gillingham in November 2010.
Just over eight years after leaving MK Dons, Murdoch has claimed his position as the manager during Wimbledon's move to Milton Keynes is the reason he has never had a permanent managerial position since.