Obtaining healthy food, free from chemical or synthetic additives, is a major challenge. In this study, we developed a preservation method using essential oils and evaluated their effect on multidrug resistant pathogenic Gram-negative bacteria. Different concentrations (1%,0.1%,0.17% and 0.35%) of Thyme oil and black seed oil were employed in this study against pathogenic E. coli and A. hydrophila in soft cheese. The used oils at a concentration of 0.1% through dipping method resulted in accepted color and odor, little effect on flavor and normal texture and appearance, while 0.1% during inoculation had the same effect as in dipping method except moderate odor. Thyme oil had the highest reduction rate in case of 1% dipping and 0.17% inoculation on A. hydrophila, while against E. coli it was found that 0.17% inoculation and 0.35% of the dipping method had the highest reduction effect. Thyme essential oil seems to be a suitable natural food preservative alternative.