Food spoilage and foodborne illnesses are two global challenges for food manufacturers. Essential oils are natural antibacterials that could have a potential for use in food preservation. Unfortunately high concentrations are needed to obtain the desired antibacterial effect, and this limits their use in food due to their adverse organoleptic properties. Encapsulation could make essential oils more effective by concentrating them in the aqueous phase of the food matrix where the bacteria are present. Here we tested encapsulation of the essential oil isoeugenol in spray-dried emulsions as a means of making isoeugenol a more effective antibacterial for use in food preservation. We used β-lactoglobulin and n-OSA starch as emulsifiers, and some emulsions were coated with positively charged chitosan to promote the contact with bacteria through electrostatic interactions. The antibacterial efficacy was quantified as the minimal bactericidal concentration in growth media, milk and carrot juice. The emulsion encapsulation system developed in this study provided high loading capacities, and encapsulation enhanced the efficacy of isoeugenol against Gram-positive and -negative bacteria in media and carrot juice but not in milk. Chitosan-coating did not enhance the efficacy further, possibly due to the aggregation of the chitosan-coated emulsions. The encapsulation system is easy to upscale and should be applicable for encapsulation of similar essential oils. Therefore, we believe it has potential to be used for natural food preservation.