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.