Division. In the following season and being continually challenged with budgetary constraints, MacPherson became the first St Mirren manager to be knocked out of both the Scottish League Cup and Scottish Cup by teams from a lower league in the same season. Despite these set-backs he retained St Mirren's SPL status with 10th place in the division. This was St Mirren's highest finish since the 1990–91 season, finishing one place above MacPherson's former club Kilmarnock and relegated Gretna. In the 2008–09 season he led St Mirren to a win over Rangers at Love Street with Stephen McGinn netting the only goal of the game. Also in the same season he led St Mirren on a run of four unbeaten games, resulting in him receiving the SPL manager of the month award for December 2008. He also guided them to the semi-finals of the Scottish Cup, beating Celtic 1–0 in the quarter finals. This result came just a week after a 7–0 defeat at Celtic Park. St Mirren were in a five club relegation battle, but a penultimate weekend win away to Falkirk, almost guaranteed safety. St Mirren stayed in the top flight on goal difference, two goals better off than Inverness. In January 2010, after Jim Jefferies left Kilmarnock, MacPherson became the longest serving manager in the SPL. On 11 May 2010, St Mirren announced that they had parted company with MacPherson. Queen of the South In June 2011, MacPherson was announced as the new manager of Dumfries club, Queen of the South on a one-year contract. His assistant manager was announced as Andy Millen. MacPherson left the club after they were relegated to the Second Division in April 2012. Queen's Park MacPherson was appointed manager of Scottish League Two side Queen's Park in January 2014. He led the "Spiders" to promotion to Scottish League One through the play-offs in his second full season in charge beating Clyde over two legs in the playoff final. The club enjoyed two seasons in the third flight before relegation via play-offs in May 2018. MacPherson left Queen's Park on 18 September 2018 to become the St Mirren technical director. He left St Mirren in August 2020. Greenock Morton In March 2021, MacPherson was appointed manager of Scottish Championship side Greenock Morton until the end of the 2020–21 season. He led the Ton to safety after winning the Scottish Championship play-offs beating Airdrieonians in