Multishell fullerenes, known as carbon nano-onions (CNOs), are an interesting class of carbon-based nanomaterials. They display several unique properties, such as a large surface area to volume ratio, a low density, and a graphitic multilayer morphology, which have made them appealing for several applications in many fields, including biology. Chemical functionalization of CNOs dramatically enhances their solubility and attenuates their inflammatory properties, thereby increasing their applicability especially in the fields of biology and medicine. CNOs functionalized with fluorescent probes can be used for cellular imaging. In this article, detailed surface characterization of CNOs functionalized with a zinc porphyrin (ZnTPP) as the fluorescent probe is presented. In particular, time-of-flight secondary ion mass spectrometry and x-ray photoelectron spectroscopy provide a detailed surface characterization of the organic functionalities introduced via “click chemistry” and clearly demonstrate the success of the CNOs functionalization process. XPS data reveal the presence of Zn and N, whilst ToF-SIMS is able to identify specific fragments related to the presence of the ZnTPP, such as the quasimolecular mass peak [C32N4H20Zn]+ and the molecular mass peak [C44N4H28Zn]+. Moreover, ions fragments deriving from the triazole ring formed by the click chemistry reaction have been identified by ToF-SIMS analysis, proving unambiguously the covalent binding of the fluorescent molecules to the CNOs surfaces.