Damaged starch typically arises from mechanical damage caused by the action of the roller mills during the wheat flour milling process. The content of resulting damaged starch in the flour significantly influences its characteristics, emphasizing the importance of understanding and controlling the formation of damaged starch for the production of specialized flours. A detailed passage analysis from three different commercial mills revealed that starch damage control is primarily achievable at front passages of the sizing and reduction system, which generate the majority of the flour release in the mill. Also, it revealed that damaged starch content increases progressively from the initial to the final passages during milling in the break, sizing and reduction system. To investigate the effects of milling parameters on damaged starch, flour yield, and energy consumption, a three-level and three-variable Box–Behnken experimental design with response surface methodology was applied. As independent variables roll gap (0.05–0.35 mm), feed rate (0.15–0.35 kg/cm min), and fast roll speed (400–800 rpm) were employed. The obtained models were utilized to optimize milling conditions for producing flours with special characteristics.