This work presents a numerical analysis of spray combustion and associated emissions formation for methyl esters of soybean (SME) and coconut (CME) in a constant volume bomb and a light-duty diesel engine. SME and CME were used to represent biodiesel fuels with high and low unsaturation levels, respectively. In the constant volume bomb, diesel engine-like conditions were used, where two ambient oxygen (O2) levels of 15% and 21% (by mole fraction) were specified to study the effects of exhaust gas recirculation on the combustion and soot formation of biodiesel fuels. As the ambient O2 level increased to 21%, the lift-off length (LOL) was reduced by 25%, while the maximum soot volume fraction (SVF) at quasi-steady state was 4 times higher. The effects of unsaturation levels were next investigated under 21% ambient O2 level. When the unsaturation level was increased, the ignition delay (ID) periods and LOL did not vary significantly as a relative difference of less than 10% was observed between both. A higher local equivalence ratio (φ) and hence maximum SVF were observed in the SME combustion. A higher adiabatic flame temperature (T) of approximately 40 K was also recorded in the SME test case. Additionally, higher soot formation and oxidation rates were found for SME. In the diesel engine cases at 21% ambient O2 level, the φ-T distributions and in-cylinder peak pressures predicted for SME and CME were identical. Meanwhile, the peak soot formation rate predicted for SME was increased by 7% as compared to that of CME. Similarly, the peak soot oxidation due to O2 calculated for SME was 30% higher than that of CME, while the oxidation rates due to hydroxyl (OH) were similar for both fuels. For the tested conditions, the rates of production of acetylene (C2H2) and nitrogen oxides (NOx) were increased by 43% and 12%, respectively, as a result of the increase in unsaturation level.