Carbon-based nanomaterials (CNMs) have attracted considerable attention in the scientific community both from a scientific and an industrial point of view. Fullerenes, carbon nanotubes (CNTs), graphene and carbon dots (CDs) are the most popular forms and continue to be widely studied. However, the general poor solubility of many of these materials in most common solvents and their strong tendency to aggregate remains a major obstacle in practical applications. To solve these problems, organic chemistry offers formidable help, through the exploitation of tailored approaches, especially when aiming at the integration of nanostructures in biological systems. According to our experience with carbon-based nanostructures, the introduction of amino groups is one of the best trade-offs for the preparation of functionalized nanomaterials. Indeed, amino groups are well-known for enhancing the dispersion, solubilization, and processability of materials, in particular of CNMs. Amino groups are characterized by basicity, nucleophilicity, and formation of hydrogen or halogen bonding. All these features unlock new strategies for the interaction between nanomaterials and other molecules. This integration can occur either through covalent bonds (e.g., via amide coupling) or in a supramolecular fashion. In the present Feature Article, the attention will be focused through selected examples of our approach to the synthetic pathways necessary for the introduction of amino groups in CNMs and the subsequent preparation of highly engineered ad hoc nanostructures for practical applications.