Diamond nanoparticles denoted as nanodiamonds (NDs) possess numerous beneficial material properties and are envisioned for a wide range of applications. In this work, complexes of polypyrrole (PPy) organic dye covalently grafted to ND surfaces are investigated by atomic scale density functional theory (DFT) computations with a view to their structural and electronic properties. NDs terminated with oxygen, hydroxyl, carboxyl, anhydride, as well as amorphous carbon (a‐C:H, a‐C:O) have been considered. Thereby the theoretical model is brought close to real nanodiamonds. Spatially separated highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) and a favorable energetic level alignment at the ND–PPy interface are observed for the majority of the oxidized NDs. This feature is also retained for NDs with amorphous surface layer. Excited states are computed by time‐dependent DFT to analyze how the electronic configuration can promote dissociation of excitons, for instance in photovoltaic applications.