The present disclosure provides methods and systems for mitigating finished product temperature transients caused by changes in product flow, raw product temperature, or other disturbances in an aseptic sterilization process. The methods and systems include applying an energy balance feedforward control scheme to the aseptic sterilization process to compensate for raw product temperature changes and changes in product flow. The methods and systems prevent damage to a finished product from occurring based on adverse transient temperature responses of heaters and coolers in an aseptic sterilization process.