The use of natural compounds as food preservatives is becoming increasingly popular as it is perceived positively by consumers. Among these substances, essential oils have attracted great interest owing to their antioxidant and antimicrobial properties. However, several challenges impair the use of essential oils in food products, such as their degradation or loss during food processing and storage, the strong aroma, even at low concentrations, which may negatively affect the sensory characteristics of food. In this context, the development of nanoformulations able to stabilize essential oils may represent a smart solution to this issue. The aim of the study was to evaluate the efficiency of alginate-based nanoformulations enriched with lemongrass (Cymbopogon nardus) essential oil (LEO) and Tween 80 against several fungi namely Penicillium expansus, Aspergillus niger and Rhizopus spp. Firstly, the flow behavior of systems at different concentrations of alginate (1%, 2% and 3% w/w) were studied. Then, emulsion-based nanoformulations at different concentrations of lemongrass essential oil in the range of 0–2% w/w were stabilized by a fixed amount of Tween 80, characterized and tested for their antifungal activity. Our results showed that the best nanoformulation able to inhibit Rhizopus spp., Penicillium expansum and Aspergillus niger, for at least 10 days, was constituted by 1% alginate/1.5% LEO/1% Tween 80. Hence, the incorporation of essential oil into nanoformulation systems may represent a valid alternative to overcome the disadvantages that limit the commercial application of essential oils.