MacGregor started out as a midfielder but also proved his versatility when he easily adapted to play at right back. However his career took a significant turn for the worse in 2001. Towards the end of the 2000/01 season Hugh Scott put Morton into administration. As a result of ongoing cash flow problems administrator Graham Martin was forced to release all of Morton's first team players. Unfortunately MacGregor was one of them. After chairman Douglas Rae stepped in to save the club from folding the team advertised for players to come for trials. MacGregor appeared at these trials and subsequently re-signed for the club.