He became coach of the Greenvale Football Club, affiliated with the Essendon District Football League in 2004, steering them to multiple Finals appearance over his six years at the club. Greevale won the Grand Final in 2007, and played off in but lost the last three Grand Final matches in 2008, 2009 and 2010. At the end of the 2010 season he was the longest-serving coach of any side in the EDFL.
At the Senior Football Presentation Night of Greenvale Football Club on 9 October 2010, MacPherson declared that he was officially stepping down as Senior Coach of the club. He had previously advised in 2009 that he would be leaving the club altogether at the end of the 2010 season, regardless of the outcome. At this point in time he has been succeeded by ex-North Melbourne Kangaroos player Anthony Rock who will undertake coaching the club in Season 2011.