Butler failed to complete the season with the MK Dons though, leaving in March 2007 after only 9 further appearances. He joined Chester City four months later and quickly struck up a strong central defensive partnership with Paul Linwood, later combining playing duties with a role on the coaching staff. But he was to rarely feature after April 2008, he fell out with Chester's manager after a poor performance against his former club Leeds United in the League Cup where Butler was substituted at half time, He never played for the club again and on 1 February 2009 he agreed a deal to leave Chester and become a free agent as he continued working towards completing his coaching qualifications.