Methods and apparatuses for encapsulating inorganic micro- or nanostructures within polymeric microgels are described. In various embodiments, viruses are encapsulated with microgels during microgel formation. The viruses can provide a template for in situ synthesis of the inorganic structures within the microgel. The inorganic structures can be distributed substantially homogeneously throughout the microgel, or can be distributed non-uniformly within the microgel. The inventive microgel compositions can be used for a variety of applications including electronic devices, biotechnological devices, fuel cells, display devices and optical devices.