The strive for mitigation of toxic pollutant emissions and carbon footprints has resulted in the incursion of many renewable alternate fuels, produced from bio-derived sources. Amongst them, biodiesel, an ester of vegetable oil, has amassed immense popularity and interest for diesel engine applications. In order to operate higher blends of biodiesel in a diesel engine, engine design modification strategies are essential. This study investigates the effect of nozzle hole geometry on the characteristics of a diesel engine fueled by biodiesel. Based on this modification, the number of nozzle holes was increased from three to five and the engine characteristics were examined for the higher blend B50 (50% kapok biodiesel + 50% diesel). Modifying the nozzle hole geometry resulted in improved combustion characteristics on account of expected enhanced fuel atomization and air/fuel mixing process. The experimental study revealed an increase in peak heat release rate and in-cylinder pressure of 32.5% and 10%, respectively, for B50 when the number of nozzle holes was increased from 3 to 5 at full load condition. Furthermore, the ignition delay was shortened with a shorter burn duration (improved combustion rate) as the number of nozzle holes is increased. The modification of nozzle hole geometry offers the benefit of improved engine performance with the increase in brake thermal efficiency of 6.1% for 5 hole nozzle geometry when compared to 3 hole nozzle geometry at full load condition. Finally, from the emissions front, HC, CO, and smoke decreased with the increase in the number of nozzle holes at the penalty of increased NOX emission.