Nanodiamonds (NDs) and graphene oxide (GO) are modern carbon-based nanomaterials with promising features for the inhibition of microorganism growth ability. Here we compare the effects of nanodiamond and graphene oxide in both annealed (oxidized) and reduced (hydrogenated) forms in two types of cultivation media—Luria-Bertani (LB) and Mueller-Hinton (MH) broths. The comparison shows that the number of colony forming unit (CFU) of Escherichia coli is significantly lowered (45%) by all the nanomaterials in LB medium for at least 24 h against control. On the contrary, a significant long-term inhibition of E. coli growth (by 45%) in the MH medium is provided only by hydrogenated NDs terminated with C-HX groups. The use of salty agars did not enhance the inhibition effects of nanomaterials used, i.e. disruption of bacterial membrane or differences in ionic concentrations do not play any role in bactericidal effects of nanomaterials used. The specific role of the ND and GO on the enhancement of the oxidative stress of bacteria or possible wrapping bacteria by GO nanosheets, therefore isolating them from both the environment and nutrition was suggested. Analyses by infrared spectroscopy, photoelectron spectroscopy, scanning electron microscopy and dynamic light scattering corroborate these conclusions.