Extensive empirical work indicates that the exhaust emission and fuel efficiency of modern common-rail diesel engines characterise strong resilience to biodiesel fuels when the engines are operating in conventional high temperature combustion cycles. However, as the engine cycles approach the low temperature combustion (LTC) mode, which could be implemented by the heavy use of exhaust gas recirculation (EGR) or the homogeneous charge compression ignition (HCCI) type of combustion, the engine performance start to differ between the use of conventional and biodiesel fuels. Therefore, a set of fuel injection strategies were compared empirically under independently controlled EGR, intake boost, and exhaust backpressure in order to improve the neat biodiesel engine cycles. For instance, the single pulse injection was applied to commensurate with the heavy EGR-incurred LTC under light loads; and the multi-pulse early injection was applied with the EGR-assisted HCCI under higher loads to facilitate the high homogeneity that is more difficult to generate with a single pulse injection. Converse to the single-shot LTC, the scheduling of the multiple fuel pulses has lesser leverage on the exact timing of combustion that may even occur before the cylinder completes compression, which may cause excessive efficiency reduction and combustion roughness. Moreover, the use of a neat biodiesel fuel may further raise the levels of hydrocarbon and carbon monoxide emissions in LTC cycles because of its higher boiling temperature range. In this research, up to 6 fuel injection pulses per cycle were applied to modulate the fuel mixing history in order to better phase the combustion thus enhance the combustion process.