Holt's results improved in 2008–09. He reached the last 16 of the 2008 Grand Prix, defeating Jimmy White and Michael Judge to qualify and scored a 5–1 defeat of Mark Allen at the venue, before losing 2–5 to Ding Junhui. In the subsequent Bahrain Championship Holt scored a 5–0 victory over David Morris in which his Irish opponent scored just 10 points, the lowest total in a best-of-nine world ranking match since 1992. He then beat Jamie Cope to reach the last sixteen and commented that he was in the best form of his career. He then lost 4–5 to Robert Milkins in the last 16, having led 3–0. He defeated Mark Davis and Dominic Dale to reach the 2009 World Championship, guaranteeing his return to the top 32. He summarised the change in his game by commenting "This year, people have had to beat me. I haven't given matches away."