We investigate the Reidemeister spectrum of direct products of nilpotent groups. More specifically, we prove that the Reidemeister spectra of the individual factors yield complete information for the Reidemeister spectrum of the direct product if all groups are finitely generated torsion-free nilpotent and have a directly indecomposable rational Malcev completion. We show this by determining the complete automorphism group of the direct product.