Thermopower measurements of molecular junctions have recently gained interest as a characterization technique that supplements the more traditional conductance measurements. Here we investigate the electronic conductance and thermopower of benzenediamine (BDA) and benzenedicarbonitrile (BDCN) connected to gold electrodes using first-principles calculations. We find excellent agreement with experiments for both molecules when exchange–correlation effects are described by the many-body GW approximation. In contrast, results from standard density functional theory (DFT) deviate from experiments by up to two orders of magnitude. The failure of DFT is particularly pronounced for the n-type BDCN junction due to the severe underestimation of the lowest unoccupied molecular orbital (LUMO). The quality of the DFT results can be improved by correcting the molecular energy levels for self-interaction errors and image charge effects. Finally, we show that the conductance and thermopower of the considered junctions are relatively insensitive to the metal–molecule bonding geometry. Our results demonstrate that electronic and thermoelectric properties of molecular junctions can be predicted from first-principles calculations when exchange–correlation effects are taken properly into account.