Antifungal activity of essential oils (EOs) of Zataria multiflora (thyme) and Syzygium aromaticum (clove) against Aspergillus flavus growth and aflatoxin B1 production was studied in potato dextrose agar (PDA) and potato dextrose broth (PDB), as well as in Iranian white cheese as a food model. The results showed that the inhibitory potential of EOs in the PDB medium is more than PDA medium. Clove EO on PDB medium prevented fungal growth and aflatoxin B1 production at 300 and 100 ppm, respectively. However, the thyme EO was not able to inhibit fungal growth completely and showed the strongest inhibition effect at 400 ppm. EOs also had more inhibitory activity in laboratory culture media than the food environments. EOs in all concentrations reduced aflatoxin B1 production and fungal growth in cheese, but only the clove EO at 150 ppm was able to prevent the fungal growth and aflatoxin B1 production completely. Thyme EO reduced aflatoxin B1 value to below detection threshold (2 ppb) at 10 μl. Our findings propose EOs as a natural inhibitor to control fungal contamination of foodstuffs such as Iranian white cheese.