A control system comprising an ammonia (NH3) storage level determination module that determines a NH3 storage level in an exhaust system, a desired NH3 storage level determination module that determines a desired NH3 storage level based on an exhaust temperature, and a nitrogen oxide (NOx) mass flow rate control module that controls a NOx mass flow rate based on a difference between the NH3 storage level and the desired NH3 storage level. A method comprising determining a NH3 storage level in an exhaust system, determining a desired NH3 storage level based on an exhaust temperature, and controlling a NOx mass flow rate based on a difference between the NH3 storage level and the desired NH3 storage level.