It is commonly reported in the literature that NOx emissions from a diesel engine increase when fuelling with biodiesel. However, some studies report varying or opposite results. This work scrutinized operating conditions known to yield both increases and decreases in NOx emissions when running on biodiesel. This involved sweeping the injection timing of an instrumented 2 L diesel engine from 14 BTDC (before top-dead-center) to 3 ATDC (after top-dead-center), under loads of 40 Nm and 80 Nm (equating to BMEP (brake mean effective pressure) of 2.5 bar and 5 bar, respectively), using ultralow sulfur diesel (ULSD) and rapeseed methyl ester (RME). Under a 40 Nm load, RME consistently generated lower NOx emissions than ULSD, whereas, under an 80 Nm load, RME generated higher NOx emissions at all but the most advanced/retarded injection timings. This behavior was linked to differences in combustion duration, ignition delay (ID), and the relative size of the premixed burn fraction (PMBF). Combustion tended to progress more quickly overall for the fuel that generated highest NOx emissions at most operating conditions. ID was always reduced when fuelling with RME, and hence PMBF was also reduced. Thus, reduced ID exerted conflicting influences over relative RME NOx emissions; a tendency to increase NOx, due to advanced start of combustion (SOC), and a tendency to decrease NOx, due to reduced PMBF. Additionally, calculations indicated that for the same SOC and PMBF RME would normally be expected to generate higher NOx emissions than UISD. However, as the level of premixing increased, the magnitude of the ceteris paribus RME NOx increase appeared to dedine. That is, as PMBF increases, the impact of the inherent factors-beyond advanced SOC- that lead to higher NOx emissions when fuelling with biodiesel appear to be reduced. This may be related to variations in soot radiative heat losses. Changes in operating PMBF may therefore explain some of the variety that exists in the literature relating to the effects of biodiesel fuelling on NOx emissions.