The aim of this investigation was to quantify organic and inorganic gas emissions from a four-cylinder diesel engine equipped with a urea selective catalytic reduction (SCR) system. Using a bench dynamometer, the emissions from the following mixtures were evaluated using a Fourier transform infrared (FTIR) spectrometer: low-sulfur diesel (LSD), ultralow-sulfur diesel (ULSD), and a blend of 20% soybean biodiesel and 80% ULSD (B20). For all studied fuels, the use of the SCR system yielded statistically significant (p < 0.05) lower NOx emissions. In the case of the LSD and ULSD fuels, the SCR system also significantly reduced emissions of compounds with high photochemical ozone creation potential, such as formaldehyde. However, for all tested fuels, the SCR system produced significantly (p < 0.05) higher emissions of N2O. In the case of LSD, the NH3 emissions were elevated, and in the case of ULSD and B20 fuels, the non-methane hydrocarbon (NMHC) and total hydrocarbon of diesel (HCD) emissions were significantly higher.