After retiring as a player, Chisholm became a coach, working in some of his roles as assistant to Ian McCall. Chisholm succeeded McCall as manager of Dundee United in 2005, and guided the club to the 2005 Scottish Cup Final, which they lost 1–0 to Celtic. He was sacked the following season, however, and was subsequently appointed manager of Scottish First Division club Queen of the South. Chisholm guided the club to the 2008 Scottish Cup Final, which they lost 3–2 to Rangers. Chisholm left Queens in 2010 to manage Dundee, but was made redundant when the club went into administration in October 2010.