Onion bulbs are typically stored at lower storage temperature for a long time, permitting their year-round availability in the market. The objective of this study was to evaluate the relationships among onion bulb quality, targeted major metabolites, and mineral nutrient contents in long-term cold-stored onion bulbs from four major different commercial onion packinghouses. Bulb fresh and dry weight, fructose, glucose, citric acid, total phenolic compounds, and ABTS were highest in Muan, compared with the other packinghouses. The contents of K, Mn, Zn, and Cu, the ratios of K/Mg, K/Ca, and Mn/Ca, and the contents of total phenolic compounds, total flavonoids, and total anthocyanins were highest in Hamyang, compared with the other packinghouses. The contents of individual free amino acids were most likely highest in Hamyang and Mungyeong packinghouses, compared with the other packinghouses. The overall responses of bulb quality, targeted major metabolites, and mineral nutrients substantially affected the differential expression pattern of principal component analysis among four commercial packinghouses. While fructose was positively correlated with glucose, it was negatively correlated with methionine, leucine, valine, isoleucine, and aspartic acid. Antioxidant activities in terms of ABTS and DPPH were negatively correlated with Mn but positively correlated with bulb dry weight, h(o), and lightness. The collective results indicate that onion bulb quality was highly affected by commercial onion packinghouses, thus glucose and fructose were highly associated with amino acids and bulb dry weight with most bulb physiological parameters. Therefore, the commercial storage facility may play a pivotal role in the fluctuation of targeted major metabolites and mineral nutrients after long-term cold storage.