The conductance of single molecule junctions is calculated using a Landauer approach combined to many-body perturbation theory MBPT) to account for electron correlation. The mere correction of the density-functional theory eigenvalues, which is the standard procedure for quasiparticle calculations within MBPT, is found not to affect noticeably the zero-bias conductance. To reduce it and so improve the agreement with the experiments, the wavefunctions also need to be updated by including the non-diagonal elements of the self-energy operator.