Oral bacterial infections are fairly common in patients with diabetes mellitus; however, due to limited treatment options, herbal medicines are considered an alternate solution. This study aimed to formulate a stable essential-oil-loaded nanoemulsion for the treatment of oral bacterial infections. Essential oils from edible sources including coriander, clove, cinnamon and cardamom were extracted by hydrodistillation. The response surface methodology was used to optimize the nanoemulsion formulation by applying the Box–Behnken design. The oil concentration, surfactant concentration and stirring speed were three independent factors, and particle size and polydispersity index were two responses. The particle size, polydispersity index and zeta potential of the optimized formulation were 130 mm, 0.222 and −22.9, respectively. The ATR-FTIR analysis revealed that there was no incompatibility between the active ingredients and the excipients. A significant release profile in active ingredients of nanoemulsion, i.e., 88.75% of the cinnamaldehyde and 89.33% of eugenol, was recorded after 24 h. In the ex vivo goat mucosal permeation study, 71.67% of the cinnamaldehyde permeated and that of the eugenol 70.75% from the nanoemulsion. The optimized formulation of the essential-oil-loaded nanoemulsion showed a 9 mm zone of inhibition against Staphylococcus aureus and Staphylococcus epidermidis, whereas in anti-quorum sensing analysis, the optimized nanoemulsion formulation showed an 18 mm zone of inhibition. It was concluded that formulated essential-oil-loaded nanoemulsion can be used against S. epidermidis and S. aureus infections in oral cavity.