Essential oils (EOs) are commonly applied in mouth care products like mouthwashes, mostly as an ethanolic solution or by usage of surfactants as solubilising agents. In this study, we present a formulation for preparation of Pickering nano-emulsions (PnE) of EOs as a novel form for application of EOs in mouth care. For the preparation of PnE, we have synthesised surface-modified silica nanoparticles with a mean diameter of 20 nm, as well as we have examined the effect of EOs concentration on PnE droplet size and stability. In vitro study of their effect on the Streptococcus mutans biofilm as the main pathogen of dental health problems has been performed. We have found that EOs in the PnE form has the highest effectiveness against biofilm formation. Diffusion through the biofilm model membrane was studied to explain this observation. We have found that PnEs have a better performance in the transportation of EOs trough model membrane than the ethanolic solutions and conventional emulsions (CEs).