Little is known about the impact of ocean acidification on predator–prey dynamics. Herein, we examined the effect of carbon dioxide (CO2) on both prey and predator by letting one predatory reef fish interact for 24 h with eight small or large juvenile damselfishes from four congeneric species. Both prey and predator were exposed to control or elevated levels of CO2. Mortality rate and predator selectivity were compared across CO2 treatments, prey size and species. Small juveniles of all species sustained greater mortality at high CO2 levels, while large recruits were not affected. For large prey, the pattern of prey selectivity by predators was reversed under elevated CO2. Our results demonstrate both quantitative and qualitative consumptive effects of CO2 on small and larger damselfish recruits respectively, resulting from CO2-induced behavioural changes likely mediated by impaired neurological function. This study highlights the complexity of predicting the effects of climate change on coral reef ecosystems.