Many potential applications of graphene require either the possibility of tuning its electronic structure or the addition of reactive sites on its chemically inert basal plane. Among the various strategies proposed to reach these objectives, nitrogen doping, i.e., the incorporation of nitrogen atoms in the carbon lattice, leads in most cases to a globally n-doped material and to the presence of various types of point defects. In this context, the interactions between chemical dopants in graphene have important consequences on the electronic properties of the systems and cannot be neglected when interpreting spectroscopic data or setting up devices. In this report, the structural and electronic properties of complex doping sites in nitrogen-doped graphene have been investigated by means of scanning tunneling microscopy and spectroscopy, supported by density functional theory and tight-binding calculations. In particular, based on combined experimental and simulation works, we have systematically studied the electronic fingerprints of complex doping configurations made of pairs of substitutional nitrogen atoms. Localized bonding states are observed between the Dirac point and the Fermi level in contrast with the unoccupied state associated with single substitutional N atoms. For pyridinic nitrogen sites (i.e., the combination of N atoms with vacancies), a resonant state is observed close to the Dirac energy. This insight into the modifications of electronic structure induced by nitrogen doping in graphene provides us with a fair understanding of complex doping configurations in graphene, as it appears in real samples. © 2015 American Chemical Society.