Fourier transform infrared spectroscopy is applied as a powerful analytic technique for the evaluation of the chemical composition of combustion aerosols emitted by off-road engines fuelled by diesel and biofuels. Particles produced by burning diesel, heated rapeseed oil (RO), RO with ethylhexylnitrate, and heated palm oil were sampled from exhausts of representative in-use diesel engines. Multicomponent composition of diesel and biofuel particles reveal the chemistry related to a variety of functional groups containing carbon, hydrogen, oxygen, sulfur, and nitrogen. The most intensive functionalities of diesel particles are saturated C–C–H and unsaturated C=C–H aliphatic groups in alkanes and alkenes, aromatic C=C and C=C–H groups in polyaromatics, as well as sulfates and nitrated ions. The distinguished features of biofuel particles were carbonyl C=O groups in carboxylic acids, ketones, aldehydes, esters, and lactones. NO2, C–N and -NH groups in nitrocompounds and amines are found to dominate biofuel particles. Group identification is confirmed by complementary measurements of organic carbon (OC), elemental carbon, and water-soluble ion species. The relationship between infrared bands of polar oxygenated and non-polar aliphatic functionalities indicates the higher extent of the surface oxidation of biofuel particles. Findings provide functional markers of organic surface structure of off-road diesel emission, allowing for a better evaluation of relation between engine, fuel, operation condition, and particle composition, thus improving the quantification of environmental impacts of alternative energy source emissions