Onions play an important part in the daily diet for most populations around the world owing to their nutritional composition and their unique capacity to naturally flavor dishes. Onions contain quercetin and its derivatives - the predominant flavonoid in onions that exert a great contribution to the effective bioactive properties of onion, including its derived products. The present paper comprehensively reviewed flavonoids (with a specific focus on quercetin in onions): their chemical composition, distribution, bioactivities in onion, and impacting factors with a focus on how they can be affected by various post-harvest conditions (storage and food processing). In addition, research on the extraction of flavonoid compounds from onions using a number of novel technologies was also reviewed.