Allium species are revered worldwide as vegetables, condiments, and spices as well as the therapeutic agents in traditional medicine. The bioactive compounds in alliums mainly include organosulfur compounds, polyphenols, dietary fibers, and saponins. Flavonoids, particularly flavonols from alliums, have been demonstrated to have the antioxidant, anticancer, hypolipidemic, anti-diabetic, cardioprotective, neuroprotective, and antimicrobial activities. However, flavonols are mostly characterized from onions and have not been comprehensively reviewed across different species. This article therefore focuses on flavonol profiles from different Allium species, their health effects, underlying molecular mechanisms, and bioavailability. Intriguingly, the functional health effects of flavonols were mainly ascribed to their antioxidant and anti-inflammatory activities involving a cascade of multiple signaling pathways. Although the Allium-derived flavonols offer tremendous potential in preventing chronic disease risks, in-depth studies are needed to translate their clinical application.