A comprehensive Raman scattering-based characterization of a full bio-based polyamide loaded with graphene nanoplatelets or layered double hydroxides (LDH) was assessed. The potential of the Raman spectroscopy was used to reveal several particularities of the nanocomposite structures induced by thermal treatment. Thus, a complete morpho-structural picture was obtained in combination with scanning electron microscopy (SEM) analysis of the neat polyamide and polyamide nanocomposites exposed at different thermal conditions (room temperature, 80 °C, and 145 °C). The analysis of G, D and 2D Raman peaks and their relative intensity ratio ID/IG, revealed the fact that the presence of graphene in polyamide is suitable for improving the essential physical properties and is also responsible for the decrease in the defects’ occurrence in the graphene layers. The surface of nanocomposites based on full bio-based polyamide, with different 2D fillers (graphenic and non-graphenic structures), was carefully evaluated before and after the thermal treatment by employing SEM and Raman analyses. The two thermal treatments allowed different chain mobility of the polymer (first temperature being over the polymer Tg and second one close to the melting phase in the viscoelastic stage). The spectroscopic and microscopic investigation was used to determine the conformational changes in filler aggregates and polymer surface, respectively.