The ability to not only control but also maintain the well-defined size of nanoclusters is key to a scientific understanding as well as their practical application. Here, we report a synthetic protocol to prepare and stabilize nanoclusters of different metals and even metal salts. The approach builds on a Pickering stabilization effect inside a microemulsion system. We prove that the emulsion interface plays a critical role in the formation of nanoclusters, which are encapsulated in situ into a silica matrix. The resulting nanocapsule is characterized by a central cavity and a porous shell composed of a matrix of both silica and nanoclusters. This structure endows the nanoclusters simultaneously with high thermal stability, good biocompatibility, and excellent photostability, making them well suited for fundamental studies and practical applications ranging from materials chemistry, catalysis, and optics to bioimaging.