The sprouts of various seeds have garnered considerable regard amid consumers due to its verdure, crispiness, and germination potential, offering a cost-effective and straightforward process. The moist and warm conditions are very conducive to germination, fostering the growth of microorganisms and thereby raising food safety concerns. The aim of the study was to investigate the impact of ozone on Enterobacteriaceae counts by subjecting wheat (Triticum aestivum) grains, alfalfa (Medicago sativa), radish (Raphanus sativus) and broccoli (Brassica oleracea) seeds to ozone gas treatment. Additionally, the grain and seeds were rinsed with ozonised water during germination. Three different treatment methods were employed for seeds and grains. In the first method, samples were exposed to ozone gas at 20 ppm for 10 minutes, with subsequent rinsing every 12 hours during germination until the rinse water appeared visually clean, at a concentration of 2.0 mg LE−1 of ozone. The second method involved rinsing with ozonised water at a concentration of 2.0 mg LE−1 for durations of 20, 40, and 60 minutes. The third method — treated with ozone gas at 50 ppm and the exposure time of 1, 2, 3, 4 and 5 h. Untreated samples were used as controls. Evaluation of the samples revealed that Enterobacteriaceae was virtually undetectable in dry seeds. However, after 72 hours of germination in both the control and ozone-treated sprouts and following 7 days of storage at 4±2 °C, Enterobacteriaceae were found at an average of 7 to 8.1 log CFU gE−1 in all samples, irrespective of the treatment method. Additionally, mould was observed only in wheat and radish sprouts during the assessment period. The study showed that there was no significant reduction in the number of mesophilic aerobic and facultative anaerobic microorganisms, moulds and Enterobacteriaceae then treated with ozone gas.