Graphene-based nanomaterials have emerged as promising materials for a wide range of applications.. Therefore, in the last years carbon nanoparticles have attracted great attention due to their low toxicity, high biocompatibility and easy preparation. Recently, N-doped carbon nanoparticles have been shown to have improved antibacterial activity over the undoped nanomaterial, but it is difficult to find correlations between the structure of the nanoparticle and its antibacterial activity. With this purpose, here, we analyze the effect of both, the nanoparticle size and the surface chemical composition of four N-doped carbon nanoparticles on the growth of Escherichia coli bacteria. Our results were analyzed using a Ligand-Substrate model based on the Monod´s equation, which allows us to interpret the dependence of the nanoparticle-bacteria affinity with the nanomaterial structure.