Keen to win another NBL championship, Mackinnon decided not to sign with West Sydney and instead signed with the re-emerging Brisbane Bullets. And although Brisbane somewhat struggled during the 2005–06 season, Mackinnon demonstrated that he was still a dominant force in the NBL by putting up career-best numbers during the 2006–07 season and led the Bullets to their first NBL championship in 20 years. He became the first player to win the MVP, Best Defensive Player and Grand Final MVP in league history in the same season.