We use scalable, effluent-free plasma functionalisation techniques to fluorinate and aminate a commercial GNP. We find that plasma fluorination adheres ~5 at.% fluorine, with minimal damage to the graphitic plane. Whereas the plasma amination adds only a modest amount of nitrogen (~ 1 at.%), but more significantly damages the GNP surface and the passivation of these new defects in air leads to a doubling in oxygen content (to ~10 at.%). However, the characterisation of these GNP is only half the story. Rather, it is the interactions between the surface chemistry and the chosen matrix that determine the ultimate morphology.