In this study, the effect of ozone treatment on the microbial population, color of the flour samples and the rheological properties of the dough (Farinograph, Extensograph and Alveograph) were evaluated in different rates of extraction (72, 83 and 90%). the flour samples were treated with ozone gas using a machine at a pressure of 1.5 bar with air capacity of 350 lit/min and a flour capacity of 2000 kg/h. The results indicated that the thermophilic and mesophilic bacteria and total mold count in ozone treated samples decreased compared to the control. The use of ozone as an oxidizing agent increased the water absorption, dough development time, the P (Dough resistance) and L (dough extensibility) parameters. The results of the color test also showed an increase in L* as lightness of ozone treated flour samples.