There is provided a system and method for controlling an engine. A request signal indicative of a demand for the engine to output a required power level is first receive. A position control signal is then generated in response to the request signal. The position request signal is indicative of a first request for adjusting a present position of a variable geometry mechanism of the engine towards a commanded position to achieve the required power level. An acceleration rate control signal is further generated on the basis of the position control signal. The acceleration rate control signal is indicative of a second request for adjusting an acceleration rate of the engine in accordance with the commanded position of the variable geometry mechanism. The position control signal and the acceleration rate control signal are then output to the engine.