Pollutant emissions are a major issue from all existing internal combustion engines, especially from Diesel engines, with nitrogen oxides (NOx) and particulate matter (PM) receiving particular attention. Simultaneous reduction of NOx and PM often presents a challenge to Diesel engine researchers because of the inherent trade-off between them due to their contradictory responses to oxygen content in a fuel. The use of liquid or gaseous biofuels in internal combustion engines, benefits in the reduction of life-cycle CO2 emissions, but suffers from unfavorable NOx/PM emissions trade-off. Hence, it is essential to moderate NOx/PM emissions trade-off in order to effectively use the Rapeseed Methyl Ester (RME) fuel as an alternative to the fossil Diesel fuel in Diesel engines. In this study, the trade-off relations among PM and NOx from a four-cylinder, direct injection (DI) Diesel engine fueled with fossil Diesel, RME, and their blends, in conjunction with various start of injection timing were investigated. It is known that when the oxygen content of the fuel increases, the PM density decreases while NOx emissions increase. But in the present study, we have proven that an improvement in NOx/PM trade-off can be achieved for pure RME fuel (B100) by adjusting the start of injection timing. The optimization of the start of injection timing (SOI) can minimize the amount of NOx emitted and reduce the density of PM produced. These results are corroborated by the use of a feedback law applied to control NOx emissions, from combustion of pure RME fuel (B100). By retarding the combustion process through optimizing the start of injection timing, this controller has proven its efficiency to track the desired trajectory of NOx and reduce the density of PM produced.