Awareness of the importance of the microbial contamination of air and surfaces has increased significantly during the COVID-19 pandemic. The aim of this study was to evaluate the presence of bacteria and fungi in the air and on surfaces within some critical areas of large supermarkets with and without an ozonation system. Surveys were conducted in four supermarkets belonging to the same commercial chain of an Apulian city in June 2021, of which two (A and B) were equipped with an ozonation system, and two (C and D) did not have any air-diffused remediation treatment. There was a statistically significant difference in the total bacterial count (TBC) and total fungal count (TFC) in the air between A/B and C/D supermarkets (p = 0.0042 and p = 0.0002, respectively). Regarding surfaces, a statistically significant difference in TBC emerged between A/B and C/D supermarkets (p = 0.0101). To the best of our knowledge, this is the first study evaluating the effect of ozone on commercial structures in Italy. Future investigations, supported by a multidisciplinary approach, will make it possible to deepen the knowledge on this method of sanitation, in light of any other epidemic/pandemic waves.