Beaton lost 4–2 to Michael Smith in the second round of the 2016 World Championship. He played in his first final since 2014 at the sixth UK Open Qualifier and was beaten 6–2 by Van Gerwen. He also made the final of the 10th Players Championship event, but lost 6–2 to Dave Chisnall. Beaton got to the quarter-finals of the 2016 World Matchplay, which was his best performance since 2001, by defeating Jelle Klaasen 10–6 and Smith 11–7. He lost 16–13 to Gary Anderson after fighting back from 9–4 down to level the match at 12–12 before eventually succumbing to the two-time reigning world champion. After Beaton took the opening set with a 135 finish in the first round of the World Grand Prix, van Gerwen won six unanswered legs to win 2–1. He lost 6–4 to Jeffrey de Graaf in the first round of the Players Championship Finals.