A method of operating an engine is provided. Output of an engine speed sensor, a mass air flow sensor, an exhaust gas temperature sensor, and an engine torque estimator are monitored with an electronic control module. It is determined if the engine is operating in one of either a transient condition and a non-transient condition based upon output of at least one of the sensors and the torque estimator. Fuel injection timing is set based upon if the engine is operating in a transient condition. An exhaust gas recirculation valve position is set upon if the engine is operating in a transient condition. An intake throttle position is set based upon if the engine is operating in a transient condition. The fuel injection timing, exhaust gas recirculation valve position, and the intake throttle position are set to minimize NOx emissions when the engine is operating in a transient condition.