Ozone applied in a low-pressure system has been studied in packed grains. In the present study, we evaluated the effect of ozone applied at low-pressures for the control of egg and larval phases of Zabrotes subfasciatus and inactivation of Aspergillus flavus in beans and possible changes in product quality. Samples of 5.0 kg of beans packed in woven polypropylene bags were exposed to ozone in the hypobaric chamber of internal volume equal to 70 L. The application of ozone was preceded by the reduction of internal chamber pressure to 50000 Pa. The ozone was then injected until the chamber's internal pressure reached 100000 Pa. An inlet ozone concentration of 61.37 mg L−1 was applied in 1, 4, 7, and 10 injections and a flow rate of 1.0 L min−1. In the control treatment, oxygen was used. The ozonation of beans with 10 injections was efficient in controlling the egg and larval phases of Z. subfasciatus, reducing mass loss and inactivation of A. flavus in the grains. The increase in the number of injections increased the electrical conductivity of the beans. However, ozone did not affect the thousand-grain mass, percentage of whole grains after cooking, total soluble solids in the cooking broth, dimensions of the orthogonal axes of the grains, volume and length-width ratio of the cooked beans. The results suggest that the number of injections in the system at low-pressure is a determining factor for the concentration of ozone inside grain packages. In this system, the application of ozone adopting 10 injections is efficient in the control of Z. subfasciatus and in the inactivation of A. flavus, without affecting the quality of the beans.