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Sutton was interviewed in January 2009 by Inverness Caledonian Thistle for the post of manager, but was unsuccessful. On 28 September 2009, Sutton was appointed manager of League Two side Lincoln City, succeeding Peter Jackson who was dismissed earlier in the month. Despite having no managerial experience, Sutton was preferred to more than 70 other applicants. Caretaker manager Simon Clark would take charge of the following day's game, with Sutton and assistant Ian Pearce to take over the day after.