This work examines the influence of essential oil composition on emulsification with rhamnolipids and their use as therapeutic antimicrobial agents against two opportunistic pathogens, methicillin-resistant Staphylococcus aureus (MRSA) and Candida albicans. Rhamnolipids, produced by Pseudomonas aeruginosa, with waste frying oil as the carbon source, were composed of eight rhamnolipid homologues. The rhamnolipid mixture was used to produce emulsions containing essential oils (EOs) of Melaleuca alternifolia, Cinnamomum verum, Origanum compactum and Lavandula angustifolia using the titration method. Ternary phase diagrams were designed to evaluate emulsion stability, which differed depending on the essential oil. The in vitro antimicrobial activity of the EOs alone and the emulsions was evaluated. The antimicrobial activity presented by the essential oils alone increased with emulsification. The surface properties of rhamnolipids contribute to the positive dispersion of EOs and thus increase their availability and antimicrobial activity against C. albicans and S. aureus. Therefore, rhamnolipid-based emulsions represent a promising approach to the development of EO delivery systems.