Cells rely on efficient quality control mechanisms to maintain the health of their organelles. Failure of these pathways contributes to aging and diseases such as Parkinson’s disease, retinal degeneration, cancer, and inherited metabolic disorders. We investigate how ubiquitin signaling regulates the function, communication, and selective autophagic turnover of peroxisomes, lysosomes, and mitochondria. By uncovering these molecular mechanisms, we aim to understand how cells preserve homeostasis and identify new opportunities for therapeutic intervention.