Flavonoids occur naturally in different types of fruits and vegetables, including tea, cabbage, cauliflower, elderberries, cranberries, red apples, lettuce, pears, spinach, green hot peppers, white and red onions, kale, blueberries, and nuts. Among these flavonoids is quercetin, a potent natural antioxidant and cytotoxic substance with a number of therapeutic functions. Nowadays, quercetin is a common ingredient in many nutraceutical and cosmeceutical products due to its antioxidant properties. Its antibacterial effects and possible action mechanisms have been explored in many studies. From these, it has been established that quercetin stops the activity of numerous Gram-negative and -positive bacteria, fungi, and viruses. This review clarifies the plant sources and extraction methods of quercetin, as well as its medicinal applications as an antibacterial, antifungal, antiviral, and antioxidant agent, with a particular emphasis on the underlying mechanisms of its biological activity. The mechanism of its antimicrobial effect involves damaging the cell membrane—e.g., by changing its permeability, preventing biofilm formation, reducing the mitochondrial expression of virulence factors, and inhibiting protein and nucleic-acid synthesis. Moreover, quercetin has been shown to impede the activity of a variety of drug-resistant bacterial strains, pointing to the possibility of using it as a strong antimicrobial substance against such strains. In addition, it has occasionally been demonstrated that specific structural alterations to quercetin can increase its antibacterial action in comparison to the parent molecule. Overall, this review synthesizes our understanding of the mode of action of quercetin and its prospects for use as a therapeutic material.