A conventional diesel engine when operated in the reactivity-controlled compression ignition (RCCI) combustion strategy faces challenges of high total hydrocarbon (THC) and carbon monoxide (CO) emissions leading to poor combustion efficiency at low engine loads. The oxides of nitrogen (NOx) versus smoke trade-off, encountered in conventional diesel combustion, is replaced by the NOx-THC trade-off in the RCCI operation. This work focuses on addressing the NOx-THC trade-off issue by systematically investigating the effects of engine control variables, such as, fuel injection timing, exhaust gas recirculation (EGR) and intake throttling, on a light duty compression ignition engine running in a methane-diesel dual fuel mode. The engine is operated at a load of 3 bar gross indicated mean effective pressure and at a speed of 1500 rev/min. Based on relationships identified between engine control variables, combustion parameters, emissions and engine performance, a bottom-up approach is used to combine the control variables synergistically to improve the NOx-THC trade-off. A combination of advanced start of injection timing of diesel (−35 degree crank angle (°CA) after top dead centre), 50% premix ratio and 55% EGR levels along with the end of port fuel injection of methane in the middle of the intake stroke (−270°CA), has resulted in a ∼34 percentage points (from 56% to 90%) improvement in combustion efficiency and a ∼9.5 percentage points improvement in thermal efficiency compared to the baseline low load dual fuel operation while maintaining good combustion stability. THC emission is reduced from 105 to ∼25 g/kWh whilst maintaining low levels of NOx (<0.3 g/kWh).