Especially in view of more and more stringent emission legislation in passenger cars it is required to reduce the amount of pollutants. In the case of Diesel engines mainly NOx and PM are emitted during engine operation. The main influence factors for these pollutants are the in-cylinder oxygen concentration and the injected fuel amount. Typically the engine control task can be divided into two separate main parts, the fuel and the air system. Commonly air system control, consisting of a turbocharger and exhaust gas recirculation control, is used to provide the required amount of oxygen and address the emission targets, whereas the fuel is used to provide the desired torque. Especially in transient maneuvers the different time scales of both systems can lead to emission peaks which are not desired. Against this background in this work instead of the common way to address the air system, the fuel system is considered to reduce emission peaks during transients. The idea is to start from a base calibration and adapt the injection parameters, like start and amount of pilot and main injection, to reduce transient emission peaks. To this end, an input shaping technique is applied to adapt parameters. The input shaping is based on an identified response model of the transient emission profile and used to generate a desired correction trajectory. By input shaping it was possible to reduce the NOx overshoot during the transient scenario while maintaining PM emissions and noise level. All experiments were performed on a 2l turbocharged common rail passenger car diesel engine at the JKU testbench and to obtain accurate NOx measurements during transients these were recorded with a highly dynamic Cambustion fNOx device.