The efficacy of ozone (O3) gas treatment to inhibit the strains growth of Aspergillus flavus and Penicillium citrinum and of aflatoxin and citrinin (CTR) to degrade in wheat grains were evaluated. The tests were performed in laboratory pilot silos containing grains artificially contaminated by these fungi or mycotoxins. Briefly, the samples were divided into control groups (no O3 gas) and O3-treated groups (40 and 60 μmol/mol), which were exposed for 30, 60, 120 and 180 min. In the highest concentration of O3 exposure (60 μmol/mol), A. flavus and P. citrinum showed complete growth inhibition after 180 min. In addition, regarding the same O3 exposure, the AFB1 and AFB2 levels were significantly reduced (12.51 and 41.06 μg/kg) when compared with control (231.88 and 265.79 μg/kg). Moreover, the CTR levels were significantly decreased after O3 treatment in both concentrations (40 and 60 μmol/mol) after 180 min of O3 exposure (103.64 and 42.90 μg/kg) when compared with control group (146.85 and 173.51 μg/kg). Practical Applications The Aspergillus flavus and Penicillium citrinum strains have been found in stored wheat grains. These fungi can be responsible for aflatoxins and citrinin formation under specific temperature and humidity storage conditions. In order to overcome this problem, ozone has been studied in laboratory scale to control fungal growth. It is possible to say that this is an attractive practice and is effective for the food industry because it decomposes to molecular oxygen without leaving residues, and furthermore is considered safe by the U.S. Food and Drug Administration.