The individual and coupled effects of the incoming free-stream turbulence (FST) and surface roughness on the transition of a separated shear layer over a flat plate is numerically investigated using Large eddy simulation (LES). The upper wall of the test section is inviscid and specifically contoured to impose a streamwise pressure distribution over the flat plate to simulate the suction surface of a low pressure turbine (LPT) blade. The interaction of the streamwise streaks due to FST and roughness with the separated shear layer is captured. The streaks induced by FST are intermittent in nature and the streaks due to roughness are steady for a given topology of the rough surface. Both FST and roughness promoted near-wall mixing. The ‘net effect’ of mixing in the pre-separated region is manifested by a shift the inflection point of the velocity profile towards the wall. This resulted in the upstream shift of the transition point and a significant reduction in the size of the separation bubble. The combined effect of FST and roughness further reduced the size of separation bubble. The streamwise evolution of the boundary layer parameters has been compared for different cases. The potential ‘roughness benefit’ obtained in the case of highly loaded turbine blades in terms of its considerable reduction of profile loss is also shown.