The results of an experimental study of nitrogen oxide (NO) and particulate matter (PM) concentrations in the exhaust gas of a compression-ignition engine used in agricultural tractors and other commercial vehicles are presented. The engine was fueled with second-generation biodiesel obtained from used frying oils (classified as waste) and first-generation biodiesel produced from rapeseed oil as well as, comparatively, diesel fuel. Tests were conducted on a dynamometer bench at a variable load and a variable engine speed. The levels of PM and NO emissions in the exhaust gas were determined. The study showed significant environmental benefits of using first- and second-generation biodiesel to power the engine due to the level of PM emissions. The PM content, when burning ester biofuel compared to diesel fuel, was reduced by 45–70% on average under the speed and load conditions implemented. As for the concentration of nitrogen oxide in the exhaust gas, no clear trend of change was shown for the biodiesel in relation to the diesel fuel. The level of NO emissions in the range of full-power characteristics was found to be lower for both tested biofuels compared to diesel fuel at lower engine speeds by an average of 7–8%, while in the range of a higher rotation speed, the NO content in the exhaust gases was higher for the tested biofuels compared to diesel oil by an average of 4–5%. The realized engine performance tests, moreover, showed an unfavorable effect of the biodiesel on the engine energy parameters. In the case of biofuels, this was by more than 4% compared to diesel fuel.