The electronic properties of sp2 carbon nanostructures are very sensitive to local perturbations, such as surface charges and adsorbed gas molecules, so that the grafting of functional groups in a controllable way has been proposed as a feasible reproducible solution for band gap engineering and controllable doping, in order to exploit and tailor the extraordinary properties of these materials. Plasma-based functionalization methods have the advantage to be solvent-free, time efficient and flexible. Within this context, we will discuss the functionalization of vertical aligned carbon nanotubes (v-CNTs) via nitrogen plasma treatment. Valence band (UPS) and scanning X-ray photoelectron spectromicroscopy (SPEM) measurements were performed at ELETTRA Synchrotron. The creation of defects induced by ions drives the grafting of nitrogen species (pyridinic, pyrrolic and graphitic) on the CNTs. A depth of functionalization up to 4 μm was evaluated by SPEM, beyond which the properties of the v-CNTs remain unperturbed. Furthermore, an intriguing different behavior of the grafting at the CNT tips with respect to the sidewalls was observed. This indicates a different reactivity of the CNT tip, where the presence of natural defects may be involved in different bonding formations between carbon and nitrogen. The effect of the temperature has been evaluated both during the plasma treatment and with post synthesis annealing, showing variations in the ratio between the nitrogen species.