Diesel engines are challenged to reduce their emissions. Nitrogen oxides (NOx), hydrocarbons, particulate matter and carbon dioxide are most important regulated diesel emissions. The legislation is driving for the use of renewable fuels in vehicles but all the impacts of those on emission control technology are not clear yet. In this study the number and chemical composition of particles emitted from a non-road diesel engine with and without a selective catalytic reduction (SCR) unit were investigated. Common diesel fuel oil (DFO) and untreated rape seed oil (RSO) were used as fuels. The NOx reduction activity of the fresh SCR catalyst was also investigated. The results indicated that the fuel had a great impact on the particles emitted from the engine. The particle number was 10–100 times higher when RSO was used as fuel compared to DFO. The DFO particles contained carbon in significantly higher proportions compared to the RSO particles. Metals, such as Fe and Cu, were also found in the DFO particles. For both fuels the NOx reduction activity was 79% with a SCR converter. As a conclusion, the use of the SCR converter decreased the number of particles in general but increased the number of the nanoparticles.