The worldwide consumption of fossil hydrocarbons in the road transport sector in 2020 corresponded to roughly half of the overall consumption. However, biofuels have been discreetly contributing to mitigate gaseous emissions and participating in sustainable development, and thus leading to the extending of the commercial utilization of internal combustion engines. In this scenario, the present work aims at exploring the effects of alternative fuels containing a blend of 15% ethanol and 35% biodiesel with a 50% fossil diesel (E15D50B35) or 50% Fischer–Tropsch (F-T) diesel (E15FTD50B35) on the engine combustion, exhaust emissions (CO, HC, and NOx), particulate emissions characteristics as well as the performance of an aftertreatment system of a common rail diesel engine. It was found that one of the blends (E15FTD50B35) showed more than 30% reduction in PM concentration number, more than 25% reduction in mean particle size, and more than 85% reduction in total PM mass with respect to conventional diesel fuel. Additionally, it was found that the E15FTD50B35 blend reduces gaseous emissions of total hydrocarbons (THC) by more than 25% and NO by 3.8%. The oxidation catalyst was effective in carbonaceous emissions reduction, despite the catalyst light-off being slightly delayed in comparison to diesel fuel blends.