Minimally processed fruits and vegetables are one of the major growing sector in food industry. Although important for their nutritional values and convenience, their composition and physicochemical properties affect their microbiological shelf life and overall quality. On the other hand, processing steps as washing, if well performed, can partially reduce the occurring microflora and the use of sanitizers are perceived negatively by the consumers. For this reasons, researchers have proposed some alternatives to the use of traditional sanitizers, such as essential oils which are complex mixtures of volatile compounds, characterized by a strong sensorial impact and produced by many plants as secondary metabolites. In this perspective, this review discusses the growing importance of minimally processed fruits and vegetables and the potential application of essential oils and their components as natural antimicrobial. Finally, the mechanisms of action of these molecules have being reviewed taking into account their use in food systems.