Nanodiamonds (NDs) emerge as excellent candidates for biological applications but their functionalization is still an issue. By analogy with hydrogenated diamond layers, an efficient and homogeneous covalent functionalization can be achieved on hydrogenated NDs. Here is reported an efficient new approach to hydrogenate NDs by reducing all various oxygenated groups into C–H terminations. The hydrogenation treatment is performed by exposing the nanoparticles to microwave hydrogen plasma in the gas phase. The hydrogenation of the nanoparticles has been carefully characterized by FTIR and XPS analysis revealing strong modification and homogenization of their entire surface. To validate this hydrogen treatment, functionalization of the NDs has been conducted by using diazonium reactions. An efficient grafting was observed for the hydrogenated NDs compared to the as-received ones.