The effectiveness of three natural compounds in slowing down the deterioration of microbial quality of Fior di latte cheese is addressed. In particular, the control of the growth of spoilage microorganisms and the determination of the Microbiological Stability Limit (MAL) were the main goals. A Central Composite Design (CCD) strategy was adopted to highlight possible combined effects between three essential oils: sage and two types of lemon. Results showed an increase in the MAL value for all cheese samples packaged with the antimicrobial compounds, compared with the control cheese. Moreover, the combinations of the three essential oils indicated that the substances can act in a synergistic or antagonistic way, depending on their concentrations. In particular, a synergistic effect was evident when the three compounds were used at about 3000 ppm.