The existing synthetic protocols for the direct functionalization of carbon-based nanomaterials often entail limitations due to their harsh reaction conditions, which require the use of high temperatures for extended periods. This study aims to overcome these limitations by developing mild and efficient synthetic protocols around 1,3-dipolar cycloaddition. Beginning with the well-established azomethine ylide derivatization, we progress to the utilization of nitrile oxide, and of nitrone derivatives for the functionalization of reduced graphene oxide (rGO) as well as of nanodiamonds (NDs). This comparative work employs both classical heating and microwave activation with the aim of reducing reaction times and enhancing efficacy. Results demonstrate that nitrone can react at 60 °C and that the reaction temperature may be decreased to 30 °C with nitrile oxide. Excellent progress was made in reducing the large excess of dipoles typically required for derivatization. Nitrile oxide was proved to be the most efficient in terms of derivatization degree, while nitrone was the most versatile reagent, facilitating the decoration of the carbon nanolayer with disubstituted dihydroisoxazole. To accurately assess the degree of functionalization, the reaction products underwent characterization using various spectroscopic and analytical techniques. Additionally, an indirect evaluation of the reaction outcome was conducted through Fmoc deprotection and quantification.