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Ozone gas (O3) is a promising alternative for fungal inactivation in agricultural commodities. This study aimed to (i) investigate the influence of airflow on the saturation of popcorn kernels with ozone gas, (ii) evaluate its effectiveness in controlling Aspergillus flavus, and (iii) analyze the quality of ozonated grains. Samples of 3.0 kg of kernels were exposed to oxygen (control) or ozone at specific flow rates of 0.15 or 1.00 m3 min−1 t−1, with an input ozone concentration of 16.0 mg L−1 for 0, 6, 12, 24, 36, or 48 h. Quality parameters assessed included expansion volume, water content, electrical conductivity, and color. At 0.15 m3 min−1 t−1, ozone consumption and saturation time were lower, with an 80% reduction in A. flavus infection after 6 h. This flow rate did not affect grain expansion or water content. Conversely, at 1.0 m3 min−1 t−1, reductions in water content and expansion were observed with extended exposure. Electrical conductivity increased in both treatments, more significantly at the lower flow rate. In conclusion, ozonation at 0.15 m3 min−1 t−1 effectively inactivated A. flavus without compromising grain quality. [ABSTRACT FROM AUTHOR]