The modification of nanodiamond (ND) surfaces has significant applications in sensing devices, drug delivery, bioimaging, and tissue engineering. Precise control of the diamond phase composition and bond configurations during ND processing and surface finalization is crucial. In this study, we conducted a comparative analysis of the graphitization process in various types of hydrogenated NDs, considering differences in ND size and quality. We prepared three types of hydrogenated NDs: high-pressure high-temperature NDs (HPHT ND-H; 0–30 nm), conventional detonation nanodiamonds (DND-H; ~5 nm), and size- and nitrogen-reduced hydrogenated nanodiamonds (snr-DND-H; 2–3 nm). The samples underwent annealing in an ultra-high vacuum and sputtering by Ar cluster ion beam (ArCIB). Samples were investigated by in situ X-ray photoelectron spectroscopy (XPS), in situ ultraviolet photoelectron spectroscopy (UPS), and Raman spectroscopy (RS). Our investigation revealed that the graphitization temperature of NDs ranges from 600 °C to 700 °C and depends on the size and crystallinity of the NDs. Smaller DND particles with a high density of defects exhibit a lower graphitization temperature. We revealed a constant energy difference of 271.3 eV between the sp-peak in the valence band spectra (at around 13.7 eV) and the sp3 component in the C 1s core level spectra (at 285.0 eV). The identification of this energy difference helps in calibrating charge shifts and serves the unambiguous identification of the sp3 bond contribution in the C 1s spectra obtained from ND samples. Results were validated through reference measurements on hydrogenated single crystal C(111)-H and highly-ordered pyrolytic graphite (HOPG).