We present a combination of density functional theory and of both non-equilibrium Green's function formalism and a Master equation approach to accurately describe quantum transport in molecular junctions in the Coulomb blockade regime. We apply this effective first-principles approach to reproduce the experimental results of Perrin et al., [Nat. Nanotechnol., 2013, 8, 282] for the transport properties of a Au–(Zn)porphyrin–Au molecular junction. We demonstrate that energy level renormalization due to the image charge effect is crucial to the prediction of the current onset in the current–voltage, I–V, curves as a function of electrode separation. Furthermore, we show that for voltages beyond that setting the current onset, the slope of the I–V characteristics is determined by the interaction of the charge carriers with molecular vibrations. This corresponds to current-induced local heating, which may also lead to an effective reduced electronic coupling. Overall our scheme provides a fully ab initio description of quantum transport in the Coulomb blockade regime in the presence of electron–vibron coupling.