A novel concept of stabilizing multiple-phase food structure such as emulsion using solely the constitutional bacteria enables an all-natural food grade formulation and thus a clean label declaration. In this paper, we propose an efficient approach to hydrophobically modifying the surface of lactic acid bacteria Lactobacillus rhamnosus (LGG) using lauroyl ahloride (LC) in non-aqueous media. Compared to the unmodified bacteria, cell hydrophobicity was dramatically altered upon modification, according to the higher percentages of microbial adhesion to hexadecane (MATH) and water contact angles (WCA) of LC-modified bacteria. No evident changes were found in bacterial surface charge before and after LC modification. By using one-step homogenization, all the modified bacteria were able to generate stabile water-in-oil-in-water (W/O/W) double emulsions where bacteria were observed on oil–water interfaces of the primary and secondary droplets. Modification using high LC concentrations (10 and 20 w/w%) led to rapid autoaggregation of bacteria in aqueous solution. A long-term lethal effect of modification primarily came from lyophilization and no apparent impact was detected on the instantaneous culturability of modified bacteria.