Biodiesel can be produced from a variety of feedstock oils and, as a result, may have a diverse set of properties based on the oil used to produce it. An understanding of the effects of these properties on engine usage and emissions is needed in order to improve biodiesel production and engine calibration. In this study, four biodiesels, produced from palm, jatropha, soybean, and beef tallow oil, are used to fuel a single-cylinder compression-ignition engine to investigate the effects of individual fuel properties on combustion phasing and behavior and exhaust emissions. This engine uses a common-rail fuel system with electronic control. Electronic control of injection is used to investigate the effects of biodiesel on combustion when combustion phasing is adjusted. Findings indicate that fuel viscosity, energy content, and molecular structure are all critical properties that alter engine combustion behavior. The combined effect of injection timing and biodiesel characteristics is found to produce lower NOx emissions compared to ultralow-sulfur diesel.