Doping of graphene-based nanomaterials with heteroatoms is a flexible and widely used approach to modify their electronic structure and chemical properties. Applications of these doped materials may imply thermal treatment, so this work was devoted to the transformations of nitrogen-containing functional groups during heating. Jellyfish-like few-layer graphene nanoflakes with the bulk and surface localization of N-groups were synthesized by different techniques: CVD growth, post-doping, CVD growth followed by oxidation, and nitric acid treatment. Synthesized materials contained a wide range of N-functionalities. The mechanism of their thermal transformations and decomposition was studied using XPS and TGA-MS. The activation energies for the decomposition of different nitrogen-containing groups were estimated by the Kissinger method.