Throughout the years, consumer demand for healthy, proper food has increased significantly. To cater the consumer demands, present trends in the food manufacturing are shifting to natural, high-quality products with decreasing processed additives changing them with plant-based substitutes. In the current study, the antibacterial activity of thyme essential oil and thyme oil-nanoemulsion (NE) was detected against E. coli O157, S. Typhimurium, S. aureus and L. monocytogenes in manufactured yoghurt. The antibacterial activities of TEO and TNE were evaluated using disc diffusion and resazurin microdilution methods. The droplets size of the TNE was 135.7±23.04 nm also, showed a greater reduction in MIC and a greater increase in zone of inhibition (ZOI) against E. coli O157 (0.04%; 36 mm), S. Typhimurium (0.01%; 41.5 mm), S. aureus (0.08%; 45 mm), and L. monocytogenes (0.01%; 31 mm). A scanning electron microscope was applied to perceive the morphological changes in the selected bacterial cells. Damage in bacterial cells following the addition of the nanoemulsion was observed. Yoghurt inoculated with the tested bacteria was supplemented with TEO and TNE at different concentrations (0.5%, 1.0%, and 2.0%) to enhance its quality. The supplementation of yoghurt with TEO nanoemulsion could represent a promising natural preservative for enhancing the microbiological safety and maintaining the sensory properties in the youghurt