Noncommunicable diseases are the leading causes of mortality worldwide. These conditions include cardiovascular and neurodegenerative diseases which require mitochondrial protection to support their respective tissues, and cancer which requires therapies that disrupt mitochondria and cells to prevent its advance. Quercetin, the most abundant flavonoid in plants and vegetables, possesses a wide range of anti-inflammatory, antioxidant, and antineoplastic properties. This review commences by a description of the metabolism, biodistribution, and pharmacokinetics of quercetin, followed by a description of its antioxidant, anti-inflammatory, and antineoplastic mechanism. The focus lies on the work done to deliver this flavonoid through nanovectors, nanoparticles specially designed for its transport and delivery, which have demonstrated enhanced effects compared to the delivery of free quercetin. Most of the literature is about the aforementioned diseases, where a special focus is placed on the exerted effects on the mitochondria. However, there are other studies, such as prevention of gastric ulcers and enhancement of sperm quality, which have used the advantages of a nanoencapsulated delivery. Finally, the nanomaterials used for quercetin delivery are reviewed and discussed in terms of their physicochemical properties and their suitability as systems for delivery and mitochondrial targeting.