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Summary: The target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, which promotes anabolic reactions and synchronously inhibits catabolic processes such as autophagy-mediated protein degradation. Its prime autophagy target is Atg13, a subunit of the Atg1 kinase complex that acts as the gatekeeper of canonical autophagy. To study whether the activities of TORC1 and Atg1 are coupled through additional, more intricate control mechanisms than simply this linear pathway, we analyzed the epistatic relationship between TORC1 and Atg1 by using quantitative phosphoproteomics. Our in vivo data, combined with targeted in vitro TORC1 and Atg1 kinase assays, not only uncover numerous TORC1 and Atg1 effectors, but also suggest distinct bi-directional regulatory feedback loops and characterize Atg29 as a commonly regulated downstream target of both TORC1 and Atg1. Thus, an exquisitely multilayered regulatory network appears to coordinate TORC1 and Atg1 activities to robustly tune autophagy in response to nutritional cues. : The target of rapamycin complex 1 (TORC1) is a master regulator of cell homeostasis, and one of its downstream targets is the Atg1 kinase complex. In the current study, Hu et al. highlight that TORC1 and Atg1 are coupled through intricate control mechanisms involving distinct bi-directional feedback loops critical for autophagy regulation. Keywords: autophagy, metabolism, kinase, phosphorylation, mass spectrometry, proteomics, Atg29, signaling