Nutrient availability plays a crucial role in plant metabolism, but its tissue-specific effects in onions (Allium cepa L.) remain poorly understood. This study aimed to elucidate the hierarchical effects of reduced nutrient supply on the metabolic profile of onion tissues, i.e., leaves, roots, and bulbs, using a multivariate metabolomics approach. Onion cultures were established in a hydroponic system, treated with Hoagland's solutions at 100 % as the control (C), and diluted solutions at 12.5 % (H12), 25 % (H25), and 50 % (H50). The metabolic signatures of onions subjected to nutrient depletion were reported by a metabolomics approach based on ultra-high-pressure liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (UHPLC/QTOF-MS). Among the treatments, H25 notably enhanced antioxidant capacity and enzyme inhibitory activities linked to neuroprotective and antidiabetic potential, particularly in bulbs. This study provides insights into optimizing nutrient management for enhanced crop quality and functionality, providing deeper insights into tissue-specific metabolic differences and the mechanisms underlying metabolite accumulation, whether through increased biosynthesis or translocation between tissues.