Autophagy is a highly conserved cellular process that degrades and recycles cytoplasmic contents and organelles through the lysosomal pathway. Protein post-translational modifications (PTMs) have emerged as key regulators of this process, with ubiquitination playing a central role in modulating multiple steps. This reversible modification, mediated by ubiquitin ligases and deubiquitinases (DUBs), enables dynamic control of autophagy. Our recent work demonstrated that, upon stimulation by reactive oxygen species (ROS), the E3 ligase TRAF6 and the deubiquitinase A20 coordinate to regulate the non-proteolytic ubiquitination of ATG9A, thereby promoting autophagy activation. Specifically, K48- and K63-linked ubiquitination of ATG9A enhances its interaction with Beclin 1 and facilitates assembly of the VPS34–UVRAG complex, leading to increased autophagic activity. Additionally, we found that knockdown of DUBs such as Leon/USP5 and USP45 augments autophagy and accelerates lysosomal degradation in both Drosophila and mammalian cells. Leon/USP5 interacts with and regulates the autophagy-initiating kinase Atg1/ULK1, while USP45 modulates actin dynamics to influence autolysosomal function. Together, these findings uncover previously unrecognized roles for E3 ligases and DUBs in controlling autophagy activation and lysosomal homeostasis.