The differences between bare carbon dots (CDs) and nitrogen-doped CDs synthesized from citric acid as a precursor are investigated, aiming at understanding the mechanisms of emission and the role of the doping atoms in shaping the optical properties. Despite their appealing emissive features, the origin of the peculiar excitation-dependent luminescence in doped CDs is still debated and intensively being examined. This study focuses on the identification of intrinsic and extrinsic emissive centers by using a multi-technique experimental approach and computational chemistry simulations. As compared to bare CDs, nitrogen doping causes the decrease in the relative content of O-containing functional groups and the formation of both N-related molecular and surface centers that enhance the quantum yield of the material. The optical analysis suggests that the main emission in undoped nanoparticles comes from low-efficient blue centers bonded to the carbogenic core, eventually with surface-attached carbonyl groups, the contribution in the green range being possibly related to larger aromatic domains. On the other hand, the emission features of N-doped CDs are mainly due to the presence of N-related molecules, with the computed absorption transitions calling for imidic rings fused to the carbogenic core as the potential structures for the emission in the green range.