Abstract The multi-dimensional computational fluid dynamics (CFD) simulation involving in-cylinder flow and combustion have been done to study the effect of soybean methyl ester and piston bowl configuration on performance, combustion and pollutant emissions from a single cylinder diesel engine. The baseline engine configuration consists of a hemispherical piston bowl. The investigation has been conducted for biodiesel blends with diesel and different piston bowl configurations such as Toroidal Re-entrant Combustion Chamber (TRCC), Re-entrant Combustion Chamber (RCC) and baseline Hemispherical Combustion Chamber (HCC) for same bowl volume to have constant compression ratio of 17.5. To simulate the in-cylinder flow and combustion process, AVL FIRE code was performed and experimental results of baseline hemispherical bowl have been used to validate the numerical model. The simulation results show that flow behaviour inside the combustion chamber strongly depends on the piston bowl configuration in diesel engine. The results obtained from the simulation for the fuel blends are compared with that of baseline diesel fuel. The brake specific fuel consumption is higher for biodiesel due to its lower heating value compared to baseline mineral diesel. However, significantly better results were obtained from engine having modified combustion chambers mainly due to better air movement and charge mixing.