Large eddy simulations (LES) of non reactive and reactive flows in a cavity-based scramjet combustor configuration from the U.S Air Force Research Laboratory (AFRL) are performed. These simulations feature a 22 species and 206 reactions chemical scheme for ethylene/air. The ability of LES to reproduce the main features found in the experiment is first emphasised such as the average velocity field and the stability of the combustion for the case studied. The influence of the mesh resolution and of the thermal wall condition on the simulation results is also investigated along with the soundness of the use of a laminar model for the filtered source terms. The results of the simulations with the finest grid (resolution of 100 micrometers in the flame region) are then employed to gain understanding in the flame dynamics. This reactive simulation shows the persistence of the two recirculation zones already present in the non reactive flow. The globally high temperature into the cavity helps to sustain a reactive zone located in the mixing layer above the cavity. Combustion first occurs in a diffusion dominated regime followed by the efficient burning of a well stirred mixture (rich then lean). A significant diffusion dominated burning is also found inside the cavity. The links between the residence time inside the cavity and the efficiency of the combustion are explored along with the velocity/heat release correlation.