The effect of pore-scale heterogeneity on non-Darcy flow behaviour is investigated by means of direct flow simulations on 3-D images of a beadpack, Bentheimer sandstone and Estaillades carbonate. The critical Reynolds number indicating the cessation of the creeping Darcy flow regime in Estaillades carbonate is two orders of magnitude smaller than in Bentheimer sandstone, and is three orders of magnitude smaller than in the beadpack. It is inferred from the examination of flow field features that the emergence of steady eddies in pore space of Estaillades at elevated fluid velocities accounts for the early transition away from the Darcy flow regime. The non-Darcy coefficient β, the onset of non-Darcy flow, and the Darcy permeability for all samples are obtained and compared to available experimental data demonstrating the predictive capability of our approach. X-ray imaging along with direct pore-scale simulation of flow provides a viable alternative to experiments and empirical correlations for predicting non-Darcy flow parameters such as the β factor, and the onset of non-Darcy flow.