Natural antioxidants, such as polyphenols, are finding increasing application in functional foods designed to improve human health, wellbeing, and performance. Quercetin is a flavonol-based polyphenol that exhibits a broad range of potentially beneficial health effects, including anti-hypertensive, anti-diabetic, anti-asthmatic, anti-carcinogenic, anti-viral and antioxidant activities. The types and amounts of quercetin found in different plant sources vary considerably. Onions have a particularly high quercetin content, mainly in the form of isoquercetin, whereas black teas and apples mainly contain quercetin in the form of rutin. Quercetin has been incorporated into different kinds of food matrices to improve their nutritional profiles, including baked goods and dairy products. However, the bioavailability of quercetin is often relatively low (<10%) because of its poor water-solubility, chemical stability, and absorption profile. The bioavailability of quercetin depends on its chemical structure, physicochemical properties, and food matrix effects. A number of studies have shown that the bioavailability of quercetin can be improved by encapsulating it in well-designed colloidal delivery systems assembled from food-grade ingredients. This review summarizes the major factors affecting the bioavailability of quercetin, as well as approaches being developed to increase its bioavailability. Enhancing the bioavailability of quercetin may lead to the development of more effective nutraceuticals and functional foods.