The synthesis of N-containing graphene derivatives by functionalization and doping of graphene oxide (GO) has been widely reported as an alternative to tune both their chemical and physical properties. These materials are of interest for a wide range of applications, including biomedicine, sensors, energy, and catalysis, to name some. Understanding the role of the nature, reactivity, concentration, and distribution of the N-based species, would pave the way towards the design of synthetic routes to obtain improved materials for specific applications. The N-groups can be present either as aliphatic fractions (amides and amines) or becoming part of the planar conjugated lattice (N-doping). Here, we have modified the distribution of N-based moieties present in N-containing RGO samples (prepared by ammonolysis of GO) and evaluated the role of the concentration and nature of the species in the thermal stability of the materials once thermally annealed (500–1050 °C) under inert environments. After these post-synthesis treatments, samples underwent marked structural modifications that include the elimination and/or transformation of N-containing fractions, which might account for the observed enhanced thermal stability. It is remarkable the formation of pyridinic N-oxide species, which role in the properties of N-containing graphene derivatives has been barely reported. The presence of this fraction is found to confer an enhanced thermal stability to the material.