Natural bioactive compounds, such as essential oils, with antimicrobial or antioxidant activity, have received considerable attention recently, especially with rising concerns on the safety of synthetic food preservatives. However, due to their low water solubility and structural stability, their incorporation into water-based food formulations are limited, as is the other lipophilic functional compounds. Moreover, in order to investigate the possible synergistic effects of the most combinations of the essential oils, the aim of this study was to prepare water-dispersible licorice-garlic-fennel essential oil nanoparticles using nanoemulsion systems through a low-energy self-emulsifying technique. The effects of essential oil proportions in the oil phase on nanoemulsion characteristics were also evaluated using a simplex-centroid mixture design, and various empirical models were developed to predict changes in the obtained nanoemulsion characteristics. Finally, multi-goal optimization was applied to obtain the most desired composite nanoemulsions with the least mean particle size, polydispersity index, turbidity, and the greatest antioxidant and bactericidal activity. Based on this optimization analysis, the most desired product was obtained using 39% licorice, 40% garlic, and 21% fennel essential oil as oil phase. The results also confirmed the synergistic effects of selected essential oils towards one another, which the nanoemulsions with two- and three- components oil phase exhibiting higher antibacterial and antioxidant activity than those with a single-component oil phase. The prepared nanoparticles had reasonable physical stability at 5 ± 1 °C during 40 days of storage.