The spatial and temporal distribution of fuel and air within the combustion chamber directly influences ignition, combustion and emissions formation in diesel engines. These fuel-air interactions are affected by details of the combustion chamber geometry and fuel injection parameters. This paper investigates the effects of piston bowl geometry and spray targeting on combustion behaviour in a single cylinder diesel engine. Closed cycle computational fluid dynamics simulations are performed on a sector mesh at various load points using the 3 Zones Extended Coherent Flame Model coupled with adaptive mesh refinement. The computational fluid dynamics model is validated experimentally at the baseline conditions at each test point after-which, parametric sweeps of bowl geometry, exhaust gas recirculation rate and nozzle tip protrusion are conducted. Results indicate that appropriately pairing fuel injection strategy and piston geometry is essential.