A muscle strain forced Mackin to miss a pre-season friendly against Shrewsbury Town in July 2008 and he returned to pre-season training later that month. He was shown a red card after picking up two yellow cards in his first appearance of 2008–09, which was Wrexham's first match in the Conference Premier, as they beat Stevenage Borough 5–0 at home on 9 August 2008. On reflection, Mackin said "As for the second yellow I felt the ball was there to be won and I thought that's what I did. Looking back now I know I should have stayed on my feet". He was handed a one-match suspension and returned in a 1–1 draw away to Rushden & Diamonds on 17 August 2008. Mackin scored his first goal of the season with a 25-yard shot against Grays Athletic, which was Wrexham's only goal in a 2–1 away defeat on 20 September 2008. Despite starting the season as a regular in the team, he found opportunities hard to come by after the arrival of Dean Saunders as manager.