Beginning the 2000/2001 season ranked 85th, MacGillivray endured a poor run of form thereafter, dropping fifty-two places to 137th by its conclusion and losing his professional status, aged 28.

He attempted to regain his place on tour in the following few seasons, but was unsuccessful; in the fifth qualifying round of the 2004 World Championship, Mehmet Husnu ended MacGillivray's run of four successive victories, defeating him 10–2.

MacGillivray's next appearance in a competitive tournament came at the 2010 World Open, where he beat fellow amateur Jamie Edwards 3–1, but lost his last-96 match 0–3 to James Wattana.

Having not entered the first four editions of the World Seniors Championship, he played in the 2015 event, beating Hassan Vaizie, 1978 UK Champion Patsy Fagan and Karl Townsend, but lost his next match 1–2 to Paul McPhillips.

During the 2015/2016 season, MacGillivray participated in the 2015 Six-red World Championship, but lost all five of his group matches - 1–5 to Yan Bingtao and Mark Davis, 2–5 to Soheil Vahedi and 3–5 to Noppon Saengkham and Stuart Bingham.