The optimal conditions for elaborating oil/water nanoemulsions of lemongrass (LG), cinnamon bark (CB) and cinnamon leaves (CL) essential oils and their antimicrobial activity against Zygosaccharomyces bailii at pH 4.00 were studied. The effect of the emulsification methodology on the physical stability and antimicrobial activity of the nanoemulsions were also evaluated. Furthermore, the sensory impact of nanoemulsions added to an apple juice was tested. LG and CL nanoemulsions were elaborated by ultrasonication and CB nanoemulsion, by high-speed homogenization. They were stable for at least 120 days at 25 °C. They exhibited antimicrobial activity against Z. bailii being CB the most effective since it showed the smallest MIC value (156.3 mg/l), followed by LG (468.8 mg/l) and CL (1250.0 mg/l). A slight increase in growth rate was observed due to ultrasonication. An additive interaction in relation to the inhibitory effect between LG and CB nanoemulsions against Z. bailii was observed. While nanoemulsions obtained would be used as natural antimicrobial agents in food and beverage products, only LG nanoemulsion at MIC concentration diluted was acceptable in juice showing the sensory impact of essential oils on foods.