The deacetylase sirtuin 3 (SIRT3) controls multiple aspects of mitochondrial function and is known to function as a tumour suppressor. Now, Verma et al. show that SIRT3 can reduce tumour cell survival by enhancing the activity of BAK and BAX, two pro-apoptotic proteins that disrupt the integrity of the outer mitochondrial membrane to cause apoptosis. Previous work had demonstrated that the mitochondrial-bound glycolytic enzyme hexokinase II prevents mitochondrial injury during apoptosis by inhibiting BAK and BAX. Here, the authors show that SIRT3 decreases the activity of cyclophilin D, which induces the detachment of hexokinase II from the mitochondria and thus enhances BAK- and BAX-induced mitochondrial injury and apoptotic cell death.