Renewable diesel fuels have the potential to reduce net CO2 emissions, and simultaneously decrease particulate matter (PM) emissions. This study characterized engine-out PM emissions and PM-induced reactive oxygen species (ROS) formation potential. Emissions from a modern heavy-duty diesel engine without external aftertreatment devices, and fueled with petroleum diesel, hydrotreated vegetable oil (HVO) or rapeseed methyl ester (RME) biodiesel were studied. Exhaust gas recirculation (EGR) allowed us to probe the effect of air intake O2 concentration, and thereby combustion temperature, on emissions and ROS formation potential. An increasing level of EGR (decreasing O2 concentration) resulted in a general increase of equivalent black carbon (eBC) emissions and decrease of NOx emissions. At a medium level of EGR (13% intake O2), eBC emissions were reduced for HVO and RME by 30 and 54% respectively compared to petroleum diesel. In general, substantially lower emissions of polycyclic aromatic hydrocarbons (PAHs), including nitro and oxy-PAHs, were observed for RME compared to both HVO and diesel. At low-temperature combustion (LTC, O2 < 10%), CO and hydrocarbon gas emissions increased and an increased fraction of refractory organic carbon and PAHs were found in the particle phase. These altered soot properties have implications for the design of aftertreatment systems and diesel PM measurements with optical techniques. The ROS formation potential per mass of particles increased with increasing engine O2 concentration intake. We hypothesize that this is because soot surface properties evolve with the combustion temperature and become more active as the soot matures into refractory BC, and secondly as the soot surface becomes altered by surface oxidation. At 13% intake O2, the ROS-producing ability was high and of similar magnitude per mass for all fuels. When normalizing by energy output, the lowered emissions for the renewable fuels led to a reduced ROS formation potential.