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Nanotechnology has impacted the food industry, mainly on developing healthier, safer, and high-quality functional food. Flavonoids are valuable compounds present in plants, fruits, grains, roots, stems, tea, and wine, among others; they possess many benefits for health due to their antioxidant properties toward reactive oxygen species, anti-inflammatory, and antiproliferative, among others. These characteristics make flavonoids attractive in various industrial areas such as medicine, nutraceutical, cosmetology, and pharmaceutical. Unfortunately, flavonoids lack long-term stability, are sensitive to light, long periods of darkness with low oxygen concentration, and often present a low water solubility and poor bioavailability. Nanoencapsulation is an alternative to improve bioavailability and sensitivity in the manufacturing process, based on encapsulating substances on a nanoscale. Nanocapsules are a promising strategy in significantly enhancing the delivery of compounds to various sites in the body. The development of biopolymers to encapsulate sensitive compounds is increasing, as well as the search for the non-toxic, biodegradable, natural and biocompatible characteristics of polymers, is fundamental. The present review describes the recent techniques and technologies for the nanoencapsulation of flavonoids. It discusses their potential advantages and possible limitations, compares natural and synthetic biopolymers, and finally, details nanoparticle regulation.