A comprehensive quantitative analysis of flavonoids, sugars, phenylalanine, and tryptophan have been carried out in different onion scales during storage at ambient temperature (20-23°C) and relative humidity (60-80 %). Depending on the length of storage, dry matter content and composition shows variation inside the onion bulbs. Inner sprouts were observed on longitudinally cut bulbs after 2 months and visible sprouts appeared after 5 months of storage. The bulbs lost 20 to 30 % of their weight at the end of the storage. Higher dry matter content was observed in the inner scales. Significantly high content of quercetin in inner scales and high level of quercetin-3,4′-O -diglucoside and quercetin-4′-O-monoglucoside in outer scales was observed during a 7 months storage. During storage period, high content of fructose and glucose was observed in the middle scales while sucrose was high in the inner scales. There was no particular trend observed within analyzed amino acids. However, the content of phenylalanine was higher than tryptophan.