Bulb onion (Allium cepa L.) contains several functional components such as quercetin glycosides, a type of flavonoid. The quercetin content of bulb onion has been determined at harvest and storage; however, little is known about the changes in quercetin accumulation during development. In this study, two yellow onion varieties, 'Momiji No. 3' and 'Quergold', which differ in quercetin content at harvest, were grown on lowland soil following spring sowing in 2018 and 2019. Then, the changes in quercetin accumulation and composition in the bulbs and leaf blades from the seedling stage to harvest were evaluated. In both years, quercetin accumulation in the bulbs followed a similar trend, with 'Quergold' tending to have a higher quercetin content than 'Momiji No. 3', except for two weeks following transplanting. Significant differences between the quercetin contents in the two varieties were observed at harvest. The content of quercetin-4'-glucoside (Q-4'-G) was the same or higher than that of quercetin-3,4'-diglucoside (Q-34'-DG) throughout development, except on October 6, 2018, and July 29, 2019, in both varieties. Meanwhile, the quercetin content per bulb increased with bulb formation in both varieties. In contrast, quercetin accumulation in the leaf blades was lower than that in the bulbs throughout development in both years. An increase was observed from July, with accumulation of Q-34'-DG dominating until early July, whereafter accumulation of both Q-34'-DG and Q-4'-G was observed until harvest. Overall, these findings suggest that accumulation of quercetin glucoside content varies dramatically with growth, differing between onion bulbs and leaf blades.