The emissions of fossil fuels derived from oil have a significant impact on the environment, climate change, air pollution, and others. Therefore, there is great interest in alternative energy sources, especially those that can reduce emissions of air pollutants. The aim of this study was the evaluation of concentration profiles of criteria pollutants, particulate matter (PM) and CO2 and unregulated pollutants (i.e., benzene, toluene, ethylbenzene, xylenes, polycyclic aromatic hydrocarbons (PAH), aliphatic hydrocarbons, aldehyde and metals) originated from burning of different fuels: The evaluated fuels were the binary mixture of fossil diesel with 5 percent biodiesel (B5), biodiesel soybean (B100), additivated biodiesel soybean (B100 adt) and additivated ethanol using a stationary diesel engine cycle, operating at the speed of 1800 rpm and 0 percent load. For a larger reliability of results, the method validation for determination the monoaromatic and aldehydes by gas chromatography flame ionization detection (GC-FID) and high-performance liquid chromatography (HPLC), respectively. PM mass was determinate by gravimetry, PAH associated to the PM were determined by gas chromatography coupled to mass spectrometry (GC-MS), aliphatic hydrocarbons were determined by GC-FID, and metals were determined by inductively coupled plasma mass spectrometry (ICP-MS). The concentration profiles were evaluated considering: 1) burning time (15, 30, and 60 minutes) and; 2) storage time (7, 14, and 21 days) at 40 Celsius Degrees to evaluate the oxidative processes that occur during storage, especially for biodiesel. When it is still cold (i.e., 15 minutes), the operation of the engine showed negative effect on particulate matter (PM), benzene, and ethylbenzene emissions for B100 compared to B5. In this study, the concentration profiles of the monoaromatic, aliphatic hydrocarbons, and PAH showed similar results to those reported in the literature, where B5 fuel emits more pollutants than pure biodiesel. However, comparing some pollutants individually, the benzene and ethylbenzene emissions were higher for B100 and B100 adt. For long engine operation periods, B5 showed the highest concentration profile for the PAH sum in the gaseous in comparison to PAH sum in the particulate phase. The storage time reduced the PM emissions in 40 percent (B100), 20 percent (B100 adt), and 3 percent (B5). Regarding the concentration of aromatics, the reduction was circa 60 percent for B100 and B100 adt. The lowest emission of pollutants was observed for additived ethanol burning.