The synthetic architectures of complex inorganic nanostructures, including multifunctional hollow capsules, are expected to play key roles in many different applications, such as drug delivery, photonic crystals, nanoreactors, and sensing. Implementation of novel strategies for the fabrication of such materials is needed because of the infancy of this knowledge, which still limits progress in certain areas. Herein we report a straightforward synthetic approach for the development of multifunctional submicron reactors comprising catalytic gold nanoparticles (2-3 nm) confined inside hollow silica capsules. Additionally, the confined growth of encapsulated metal nanoparticles was carried out to evidence the usefulness and functionality of these reactors in catalytic applications and as an approach for the development of novel complex nanostructures. Their potential and multifunctionality have been pointed out by fabrication of SERS-encoded submicrometer particles with shape and size uniformity for use in antigen biosensing; this was accomplished via codification of gold nanoparticle islands grown onto their inner surfaces.