The purpose of the study was to investigate the decomposition of onions under anaerobic and aerobic conditions. The main aim was to determine the changes in composition of quercetin-related compounds and sugars, with simultaneous analysis of total phenolics, total flavonoids and antioxidant activity. The results indicate that anaerobic conditions lead to the deterioration of onions, along with a gradual decrease in quercetin glucoside content. However, the quercetin aglycone increased simultaneously to 0.64 μmol g −1 fresh weight (FW) during the 10th week, while the fresh onions contained 0.06 μmol g −1 FW. The total sugar content decreased incessantly, while the total phenolics and flavonoids increased to 7080.67 ± 1248.20 μg gallic acid equivalents g −1 FW and 2340.10 ± 203.47 μg quercetin equivalents g −1 FW, respectively, during the 10th week. Under the aerobic condition, the total quercetin content was found to increase slowly but had a tendency to decrease during storage. The sugar content increased up to 6 weeks, followed by its gradual decrease. In addition, the total phenolics, flavonoids and antioxidant activity exhibited a decline during 1 month, with their highest content being observed during the 8th week.