Metal atom clusters constitute very promising candidates as luminophores for applications in biotechnology because they are nanosized entities offering robust luminescence in the near-infrared field (NIR). However, they cannot be used as prepared for biological applications because of potential toxic effects and quenching of the clusters' luminescence in aqueous media, and they therefore need to be dispersed in a biocompatible matrix. We describe herein the encapsulation of octahedral rhenium clusters, denoted as A(4)[Re(6)Q(8)L(6)] (A = Cs or K, Q = S or Se, and L = OH or CN), in silica nanoparticles by a water-in-oil microemulsion process, paying particular attention to the clusters' stability. The obtained A(4)[Re(6)Q(8)L(6)]@SiO(2) nanoparticles are 30 nm in size with good monodispersity and a perfectly spherical shape, as shown by scanning electron microscopy (SEM). The presence of cluster units inside the silica matrix was evidenced by scanning transmission electron microscopy in annular dark-field mode (ADF-STEM). From the point of view of their optical properties, the A(4)[Re(6)Q(8)L(6)]@SiO(2) nanoparticles show red and NIR emission under UV excitation, even when dispersed in water. The evolution of the structural and luminescence properties of clusters before and after encapsulation was followed by Raman and photoluminescence spectroscopy.