The present study has allowed us to describe the chemical composition of commercial orange, lemon and mandarin EOs, and to examine and compare their antimicrobial activity, growth inhibition and microbial inactivation. The disk diffusion method might not be an adequate tool for selection among EOs with the best antimicrobial activity. However, the determination of the MIC and MBC by the tube dilution method revealed a different antimicrobial pattern for the three EOs as a function of the microorganism investigated. Despite the uneven result obtained when evaluating the antimicrobial activity of the three EOs acting alone, their efficacy improved when they were combined with mild heat treatment, showing valuable synergistic lethal effects that allowed us to inactivate more than 5 log cycles of E. coli O157:H7 and L. monocytogenes EGD-e cells at pH 7.0. Consequently, a proper evaluation of antimicrobial activity of EOs has demonstrated alternatives to improve traditional heat treatments in order to reduce treatment intensity and, thus, adverse effects on food characteristics. Further studies are required to describe how the antimicrobial activity of these EOs is affected by environmental factors such as treatment medium pH or food composition. The application of these citrus EOs might specially be recommended to improve the pasteurization process of fruit juices or fruit-based drinks. Finally, our study points out the interest in taking profit from waste products of the juice industry, maximizing the use of existing resources and minimizing adverse effects of by-products in the environment.