Flavonoids are a large and diverse group of polyphenolic compounds with antioxidant effects. While the flavonoid content and composition profile clearly reflect the genetic background of the cultivar, environmental conditions and agronomic practices are also determinants for the composition of crops at harvest. Considerable research has been directed toward understanding the nature of polyphenols in different products and the factors influencing their accumulation. This review examines the flavonoids as a class of compounds, the role these compounds play in the plant, their contributions to product quality, and recent research on the impacts of environmental factors and cultural practices on flavonoid content in onions, highlighting how this knowledge may be used to modulate their polyphenolic composition at harvest or during post-harvest handling.