In this study, we investigated the mutual influence of metal nanoparticles and the color centers in lithium and sodium fluorides based on absorption spectroscopy, infrared spectroscopy, atomic force microscopy, and photoluminescence method. Atomic force images of the fresh cleavage of the γ-irradiated and photo-bleached single crystal of sodium fluoride indicated the photo-induced aggregation of F color centers followed by the formation and integration of sodium nanoparticles. The thermo-induced changes in the photo-bleached samples exhibited the inverse trend, i.e., disintegration of the nanoparticles and restoration of a crystal lattice. In the photo-bleached γ-irradiated lithium fluoride crystals, we detected the luminescence of F3 centers and confirmed that the mechanism of nanoparticle formation was due to aggregation of the color centers.