Muir was re-elected in 2006. On June 26, 2006, MacDonald shuffled his cabinet, moving Muir to Minister of Service Nova Scotia and Municipal Relations. In October 2007, Muir was given an additional role in cabinet as chair of the Treasury and Policy Board. Muir announced on December 29, 2008, that he would not reoffer in the next election, and was shuffled out of cabinet on January 7, 2009. He returned to cabinet on March 10, 2009, taking over as Minister of Finance and Minister of Aboriginal Affairs, following the death of Michael Baker.