Functional silica nanoparticles and in particular luminescent silica nanoparticles constitute very promising candidates for many applications in the field of biotechnology, theranostics, and photonics. However, optimizing the design of such materials requires a deep understanding of their physicochemical properties. In this article are reported extended investigations on luminescent Cs 2 [Mo 6 Br 14 ]@SiO 2 nanoparticles prepared by a water-in-oil microemulsion technique. We bring here new insights into the structure of such nanoparticles and its interplay with their optical properties. The structural interactions between the cluster units and the silica matrix were investigated and are discussed in details on the basis of FE-SEM, HAADF-STEM, ICP-OES, BET, 29 Si MAS NMR, and photoluminescence studies. As part of the risk evaluation before potential applications, the toxicity of the nanoparticles both on plants and on human cells was evaluated.