On 5 June 2013, it was announced that MacDonald had signed with recently relegated SPL side Dundee with fellow former Morton full-back Willie Dyer. MacDonald scored his first goal for The Dees in a 5–0 win at Clyde in a pre-season friendly. On the first day of the SPFL Championship, "Peaso" put Dundee ahead against Queen of the South, but they lost the game 4–3 at Palmerston. He then netted twice at Dens in extra time to put Dundee past Forfar in the Ramsdens Cup, then put another past them in the League Cup, a free kick in the dying moments of extra time. The striker scored again when Livingston came to Dens, hit a penalty in against Stenhousemuir in the Ramsdens Cup, then another in a shootout. His next goals came against his former club Morton when he scored twice.
MacDonald was proving to be a key player as Dundee pushed for the top of the league, and scored four goals in three games, twice away to Dumbarton, once more against Queen of the South, then in a 2–1 defeat at Livingston where he also missed a penalty. When Dundee visited Hamilton hoping to reel in the team top of the league, "Peaso" struck with a diving header in the last few minutes after a shot from Martin Boyle had come off the bar to give the Dees a 3–0 win. He rounded off 2013 with a goal against Alloa then another two against Dumbarton. The 33-year-old had to wait until the 1st of March for his next goal in a 2–0 win against his former employers Morton, with new manager Paul Hartley now in charge. He scored again a fortnight later when The Dark Blues visited Livingston, a curling free kick to keep Dundee top of the league in a 2–0 victory.
MacDonald was released by Dundee in January 2015