Flavonoids are secondary products of plants that include thousands of compounds classified in several classes. Preclinical studies mainly carried out in rodents suggest that they may have a role in the prevention of immunoglobulin E (IgE) synthesis and mast cell degranulation. Interestingly, using animal models with allergic asthma, it can be concluded that preventive treatment with particular flavonoid classes can reduce airway hyperresponsiveness, which is accompanied by lowered inflammatory mediators such as histamine and cytokines, and cell infiltration. In addition, there are some clinical trials in patients with allergic asthma or rhinitis that offer promising results with regard to these natural compounds. On the other hand, the dissection of cellular mechanisms that have interacted with flavonoids allow their effectiveness to be understood. Among these mechanisms there is a lower expression of IgE receptor or other membrane receptors, the modulation of calcium influx, and the downregulation of particular signaling pathways that eventually produces lower primary and secondary mediator release. In conclusion, some particular flavonoids could be an alternative or complementary therapy in the prevention and treatment of some allergies. Nevertheless, an increased number of clinical trials is required in order to confirm the therapeutic role of flavonoids.