Caused by the demanding and more and more stringent legislated emission limits for passenger car engines, the effect of transient emission peaks becomes more and more important for the overall emission limits. In case of Diesel engines, the two main concerned pollutants are NOx and PM and typically the compliance with the legislation is achieved by a suitable control of the fuel and air system of the engine. Especially during transients the coordination of both loops is crucial for the overall performance. Typically the control is separated in the two loops, where coupling effects and different time scales and dynamics can lead to undesired overshoots during transients. Against this background in this work an input shaping technique to reduce the transient emission peaks is proposed. The input shaping is based on an identified response model of the transient emission profile and used to determine suitable correction trajectories which can be applied to an existing calibration and reduce undesired effects during transients while allowing to keep the base calibration and control structure of the engine control unit. In this study input shaping is applied for the rail pressure and injection parameters to reduce the NOx emissions while the PM emissions, efficiency and noise levels should be kept similar to the nominal operation. The proposed strategy is evaluated on a 2l turbocharged common rail passenger car Diesel engine mounted at a dynamic engine testbench and promising results are achieved.