Autophagy is regulated by stimuli, including developmental signals such as the steroid hormone ecdysone in flies and environmental cues such as nutrient deprivation. This study shows that in the Drosophila melanogaster fat body, autophagy is inhibited by Hox proteins — transcription factors that drive morphogenesis along the anterior–posterior axis. The authors found that Hox genes are downregulated at the onset of developmental autophagy and following starvation, suggesting that Hox proteins inhibit autophagy. Temporal Hox expression was decreased by ecdysone (developmental)-mediated as well as target of rapamycin and insulin receptor (starvation)- mediated downregulation of Pontin (a known component of the Brahma chromatin remodelling complex that maintains Hox gene expression). Finally, Hox proteins repressed Atg and other autophagy genes to inhibit autophagy. Thus, in addition to providing spatial information during development, Hox proteins act as temporal negative regulators of autophagy.