The present paper describes the results of an experimental study performed burning alternative fuels, different per quality and feedstock, in a modern diesel engine compliance the Euro 5 emission standards. Three alternative fuels were tested on the engine and compared with a reference fossil fuel in terms of combustion characteristics, fuel consumption, noise and emissions. The alternative fuels were two biodiesels (RME and SME) and a Fischer–Tropsh (GTL), while the reference fuel was an EU certification diesel fuel. The engine employed in the study was a light-duty diesel engine developed for passenger car and light truck application, and equipped with the new generation ECU able to drive the engine under ‘‘torque-controlled” mode by means of instrumented glow-plugs with pressure sensor. The experiments were carried out in a fully instrumented test bench fuelling the engine with the various fuels. The tests were done in a wide range of engine operation points for the complete characterization of the biodiesels performance in the NEDC cycle. Moreover, the trade-off NOx–PM by EGR sweep in the three most critical test points for the engine emission performance was carried out for all fuels. The test methodology was selected carefully in order to evaluate the interaction between the fuel quality and the engine management strategy. The results put in evidence a strong interaction between the alternative fuel quality and the engine control mode highlighting the great benefits reachable by exploiting simultaneously the alternative fuel quality and the flexibility of the new engine management strategies.