Dual fuel engines constitute a viable solution for enhancing the environmental sustainability of the shipping operations. Although these engines comply with the Tier III NOx emissions regulations when operating at the gas mode, additional measures are required to ensure such compliance at the diesel mode. Hence, this study aimed to optimise the settings of a marine four-stroke dual fuel (DF) engine equipped with exhaust gas recirculation (EGR) and air bypass (ABP) systems by employing simulation and optimisation techniques, so that the engine when operating at the diesel mode complies with the ‘Tier III’ requirements. A previous version of the engine thermodynamic model was extended to accommodate the EGR and ABP systems modelling. Subsequently, a combination of optimisation techniques including multiobjective genetic algorithms (MOGA) and design of experiments (DoE) parametric runs was employed to identify both the engine and the EGR/ABP systems settings with the objective to minimise the engine brake specific fuel consumption and reduce the NOx emissions below the Tier III limit. The derived simulation results were employed to analyse the EGR system involved interactions and their effects on the engine performance and emissions trade-offs. A sensitivity analysis was performed to reveal the interactions between considered engine settings and quantify their impact on the engine performance parameters. The derived results indicate that EGR rates up to 35% are required, so that the investigated engine with EGR and ABP systems, when operating at the diesel mode, achieves compliance with the ‘Tier III’ NOx emissions, whereas the associated engine brake specific fuel consumption penalty is up to 8.7%. This study demonstrates that the combination of EGR and ABP systems can constitute a functional solution for achieving compliance with the stringent regulatory requirements and provides a better understating of the underlined phenomena and interactions of the engine subsystems parameters variations for the investigated engine equipped with EGR and ABP systems.