Nowadays, emissions from internal combustion engines are a relevant topic of investigation, taking into account the continuous reduction of emission limits imposed by environmental regulatory agencies around the world, obviously as the result of earnest studies that have pointed out the impact on the human health of high levels of contaminants released into the environment. Over recent years, the use of biofuels has contributed to attenuating this environmental issue; however, new problems have been raised, such as NOx emissions tend to increase as the biofuel percentage in the fuel used in engines increases. In this research, the emissions of a compression ignition internal combustion engine modeled as a variable volume reactor with homogeneous combustion were numerically investigated. To analyze the combustion process, a detailed kinetics model tailored specifically for this purpose was used. The kinetics model comprised 30,975 chemical reactions involving 691 chemical species. Mixtures of fuel surrogates were then created to represent the fuel used in the Brazilian fuel marketplace, involving (i) fossil diesel—“diesel A”, (ii) soybean diesel—“biodiesel”, and (iii) hydrotreated vegetable oil— “HVO”. Surrogate species were then selected for each of the aforementioned fuels, and blends of those surrogates were then proposed as mixture M1 (diesel A:biodiesel:HVO—90:10:0), mixture M2 (diesel A:biodiesel:HVO—85:15:0), and mixture M3 (diesel A:biodiesel:HVO—80:15:5). The species allowed in the kinetics model included all the fuel surrogates used in this research as well as the target emission species of this study: total hydrocarbons, non-methane hydrocarbons, carbon monoxide, methane, nitrogen oxides, carbon dioxide, soot, and soot precursors. When compared to experimental trends of emissions available in the literature, it was observed that, for all the proposed fuel surrogates blends, the numerical approach performed in this research was able to capture qualitative trends for engine power and the target emissions in the whole ranges of engine speeds and engine loads, despite the CO and NOx emissions at specific engine speeds and loads.