We studied the feasibility of monitoring and controlling the manufacturing process of an infant formula with rice starch by testing in-process samples using rheology. We used DSC to first determine the gelatinization temperature of the rice starch, a key ingredient of this product. With this characteristic temperature and the process design known, rheological measurements were conducted on the in-process samples for detecting the presence and extent of gelatinization and retrogradation of rice starch; in-process samples were collected from the carbohydrate tank, after the homogenizer, and the finished product tank. The correlation between the rheological measurements on these samples and manufacturing performance proved that rheology is a very sensitive tool for monitoring the structural development of this infant formula during main process, and their influence on sterilization efficiency. We observed that the lower degree of gelatinization during main process, a shorter residence time in the finished product tank, and using caustic flush rather than clean-in-place additively lead to higher sterilization efficiency. These findings can be utilized for a rational design and analysis of the manufacturing process for infant formulas containing rice starch.