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The modern food industry seeks to produce ecologically healthy and clean food products. However, finding effective means of storing raw materials without losing their quality is still a major problem faced by the industry. One of the promising methods on long-term storage of grain bases for good quality and safety is the ion-ozone cavitation treatment. Therefore, this study aims to determine the influence of various ion-ozone treatment parameters on the quality and safety factors of millet, buckwheat, chickpea, and lentil grain bases at the Food Quality and Safety Assessment Laboratory, Almaty University of Technology, Almaty, Kazakhstan. With ozonation, the buckwheat grain bases showed a significant increase in fatty acids, the millet and chickpea grains showed a slight increase, while the lentil seeds exhibited a slight decrease in fatty acids compared to the control. Overall, by treating with a low concentration of ion-ozone, the buckwheat showed fewer microorganisms; in chickpea grains the molds and yeast did not develop; in millet grains the yeast was absent and molds were not higher than control; and in lentil grain bases, the permissible yeast growth with no molds was observed. The storage life of extruded grain bases after ion-ozone cavitation treatment increased by a minimum of 60 days (millet) and to more than 240 days (buckwheat). The optimum basic parameters were determined, ensuring a maximum shelf life of up to eight months without losing the quality of the cereals and legume grain products. The said procedure was found as an effective measure for long-term storage of the extruded grain bases with sustainable safety and quality.