A modern diesel engine is a reliable and efficient mean of producing power. A way to reduce harmful exhaust and greenhouse gas (GHG) emissions and secure the sources of energy is to develop technology for an efficient diesel engine operation independent of fossil fuels. Renewable diesel fuels are compatible with diesel engines without any major modifications. Rapeseed oil methyl esters (RME) and other fatty acid methyl esters (FAME) are commonly used in low level blends with diesel. Lately, hydrotreated vegetable oil (HVO) produced from vegetable oil and waste fat has found its way into the automotive market, being approved for use in diesel engines by several leading vehicle manufacturers, either in its pure form or in a mixture with the fossil diesel to improve the overall environmental footprint. There is a lack of data on how renewable fuels change the semi-volatile organic fraction of exhaust emissions. In order to characterize and explain the difference in exhaust emissions from fossil diesel, HVO and RME fuels, particulate matter (PM) emissions were sampled at two exhaust positions of an experimental single cylinder Scania D13 heavy-duty (HD) diesel engine: at the exhaust manifold, and after a diesel oxidation catalyst (DOC). Advanced analyzing techniques were used to characterize the composition of the organic PM. Special attention was paid to an operating point at 18% intake oxygen level with constant engine operating conditions where the emission level of nitrogen oxides (NOx) was low, and carbon monoxide (CO) and total hydrocarbon (THC) were relatively low. On-line aerosol mass spectrometry (AMS) suggests that the chemical composition of the organic aerosols (OAs) was similar for HVO and diesel. However, RME both reduced the OA emissions and changed the composition with evidence for fuel signatures in the mass spectra. When the emissions were aged in an oxidation flow reactor to simulate secondary organic aerosol (SOA) formation in the atmosphere, it was found that OA concentration strongly increased for all fuels. However, SOA formation was substantially lower for RME compared to the other fuels. The DOC strongly reduced primary organic emissions in both the gas (THC) and particle phase (OA) and only marginally affected OA composition. The DOC was also effective in reducing secondary organic aerosol formation upon atmospheric aging.