Gold nanoparticles with only a few atoms, known as gold nanoclusters (AuNCs), have dimensions below 2 nm and feature singular properties such as size dependent luminescence. AuNCs are also highly photostable and have catalytic activity, low toxicity and good biocompatibility. With these properties, they are extremely promising candidates for application in bioimaging, sensing and catalysis. However, when stabilized only with small capping ligands, their use is hindered by lack of colloidal stability. Encapsulation of the AuNCs can contribute to provide a more robust protection and even to improve their properties. Here, we review the encapsulation of AuNCs in polymers, silica and metal organic frameworks (MOFs) for applications in bioimaging, sensing and catalysis.