This study investigates the mechanism by which Tor, a phosphatidylinositol kinase-related kinase, regulates autophagy in *Saccharomyces cerevisiae*. The authors found that the protein kinase activity of Apg1, an essential component of the autophagy pathway, is enhanced by starvation or rapamycin treatment. Additionally, they discovered that Apg13, which binds to and activates Apg1, is hyperphosphorylated in a Tor-dependent manner, reducing its affinity for Apg1. This association between Apg1 and Apg13 is crucial for autophagy but not for the cytoplasm-to-vacuole targeting (Cvt) pathway, another vesicular transport mechanism. Other Apg1-associated proteins, such as Apg17 and Cvt9, are specifically involved in autophagy and the Cvt pathway, respectively, suggesting that the Apg1 complex plays a key role in switching between these two transport systems in a nutrient-dependent manner. The study also demonstrates that the Apg1–Apg13 complex is required for autophagy induction, and that Tor signaling negatively regulates Apg1 kinase activity through the (hyper)phosphorylation of Apg13. These findings provide insights into the regulation of autophagy and the interplay between nutrient sensing and vesicular transport pathways in yeast.This study investigates the mechanism by which Tor, a phosphatidylinositol kinase-related kinase, regulates autophagy in *Saccharomyces cerevisiae*. The authors found that the protein kinase activity of Apg1, an essential component of the autophagy pathway, is enhanced by starvation or rapamycin treatment. Additionally, they discovered that Apg13, which binds to and activates Apg1, is hyperphosphorylated in a Tor-dependent manner, reducing its affinity for Apg1. This association between Apg1 and Apg13 is crucial for autophagy but not for the cytoplasm-to-vacuole targeting (Cvt) pathway, another vesicular transport mechanism. Other Apg1-associated proteins, such as Apg17 and Cvt9, are specifically involved in autophagy and the Cvt pathway, respectively, suggesting that the Apg1 complex plays a key role in switching between these two transport systems in a nutrient-dependent manner. The study also demonstrates that the Apg1–Apg13 complex is required for autophagy induction, and that Tor signaling negatively regulates Apg1 kinase activity through the (hyper)phosphorylation of Apg13. These findings provide insights into the regulation of autophagy and the interplay between nutrient sensing and vesicular transport pathways in yeast.