He made a good start to the 2012–13 season, beating Tony Drago and Robert Milkins to qualify for the final stages of the Australian Goldfields Open in Bendigo; there he beat local wildcard James Mifsud 5–0, before exiting the tournament by the same scoreline against Ding Junhui. At the 2013 Welsh Open, McManus reached his first quarter-final since the 2006 Grand Prix, with a 4–2 win over the number 16 seed Barry Hawkins, followed by a dramatic comeback to beat Joe Perry 4–3, after having trailed 0–3. He was beaten in the quarter-final 3–5 by compatriot Stephen Maguire. The following tournament, the Haikou World Open, saw McManus win three matches in qualifying to reach the latter stages of the tournament; he then beat local wildcard Lin Shuai 5–3, before facing compatriot John Higgins. McManus put in a good performance; he ultimately lost 3–5, but picked up valuable ranking points in the process.