In this study, we present an innovative ion-beam doping technique for the controlled modification of the near-surface region of multi-walled carbon nanotubes (MWCNTs) aimed at creating pyridinic and pyrrolic nitrogen defects in their walls. This method involves the irradiation of MWCNTs with nitrogen ions using a high-dose ion implanter, resulting in the incorporation of nitrogen atoms into the nanotube structure. The structural and chemical changes induced by the ion-beam treatment were thoroughly characterized. Scanning electron microscopy (SEM) analysis revealed subtle changes in nanotube morphology, while X-ray diffraction (XRD) measurements exhibited altered peak intensities and a shift in the (002) reflection peak, indicating structural modifications, which correlates with transmission electron microscopy (TEM) data. X-ray photoelectron spectroscopy (XPS) analysis confirmed the successful embedding of nitrogen, mainly in pyridinic and pyrrolic configurations, as evidenced by the presence of corresponding lines in the N1s spectrum. Our findings demonstrate the feasibility of precisely engineering nitrogen defects in MWCNTs using the ion-beam doping technique. This approach is expected to be promising for the use of carbon nanotubes surface-functionalized with nitrogen atoms in the development of new devices for electronics, electrochemistry, catalysis, etc.