The negatively charged germanium-vacancy GeV− color centers in diamond nanocrystals are solid-state photon emitters suited for quantum information technologies, bio-sensing, and labeling applications. Due to the small Huang–Rhys factor, the GeV−-center zero-phonon line emission is expected to be very intensive and spectrally narrow. However, structural defects and the inhomogeneous distribution of local strains in the nanodiamonds result in the essential broadening of the ZPL. Therefore, clarification and elimination of the reasons for the broadening of the GeV− center ZPL is an important problem. We report on the effect of reactive ion etching in oxygen plasma on the structure and luminescence properties of nanodiamonds grown by hot filament chemical vapor deposition. Emission of GeV− color centers ensembles at about 602 nm in as-grown and etched nanodiamonds is probed using micro-photoluminescence and micro-Raman spectroscopy at room and liquid nitrogen temperature. We show that the etching removes the nanodiamond surface sp2-induced defects resulting in a reduction in the broad luminescence background and a narrowing of the diamond Raman band. The zero-phonon luminescence band of the ensemble of the GeV− centers is a superposition of narrow lines originated most likely from the GeV− center sub-ensembles under different uniaxial local strain conditions.