This paper presents a frequency-domain methodology for robust systemcontrol design, and its application in airpath control of a real turbocharged Diesel engine with intake throttle and exhaust gas re-circulation system. The objective is to find a robust control-system which reduces pollutant emission. The three inputs (throttle, wastegate and EGR valves) and two outputs (airflow and boost pressure) of the airpath make the system complex. AMulti InputMulti Output (MIMO) fractional order approach called CRONE (French abbreviation which means robust control of a non integer order) is used to design a non-square control-system for this non-linear plant. Firstly, a multisine signal is used for the system-identification, the airpath inputs are excited around all operating points in order to find a linear model of the plant. Then, the frequency responses of a defined nominal plant and experimental plant are taken into account to design the MIMO control-system using the CRONE shaping approach which permits to maintain performance and robust stability around a wide set of operating points. Finally, pollutant emission results from a driving cycle in test-bench show the relevance of the proposed approach.