The ubiquitin-proteasome system (UPS) is a fundamental regulatory mechanism maintaining cellular proteostasis through the targeted degradation of proteins. Beyond its canonical role in protein turnover, the UPS governs diverse biological processes, including cell cycle control, DNA repair, immune responses, and stress adaptation. Dysregulation of UPS components is increasingly recognized as a driving force in the pathogenesis of numerous diseases, such as cancer, neurodegenerative disorders, metabolic dysfunctions, and infections. In plants, the UPS also plays a pivotal role in environmental stress responses and hormone signaling, offering promising avenues for crop improvement. This review presents a comprehensive overview of the molecular architecture and functions of the UPS, explores its role in maintaining cellular and systemic homeostasis, and critically examines the consequences of UPS dysfunction across various disease contexts. We further highlight emerging technologies, including ubiquitinomics, CRISPR-based screens, and targeted protein degradation platforms, that are accelerating UPS research. Finally, we discuss current challenges and future opportunities for translating UPS insights into therapeutic and biotechnological innovations. A deeper understanding of the UPS across biological systems is essential for developing next-generation strategies to combat human diseases and enhance agricultural resilience.