Silica nanocapsules have attracted significant interest due to their core-shell hierarchical structure. The core domain allows the encapsulation of various functional components such as drugs, fluorescent and magnetic nanoparticles for applications in drug delivery, imaging and sensing, and the silica shell with its unique properties including biocompatibility, chemical and physical stability, and surface-chemistry tailorability provides a protection layer for the encapsulated cargo. Therefore, significant effort has been directed to synthesize silica nanocapsules with engineered properties, including size, composition and surface functionality, for various applications. This review provides a comprehensive overview of emerging methods for the manufacture of silica nanocapsules, with a special emphasis on different interfacial engineering strategies. The review starts with an introduction of various manufacturing approaches of silica nanocapsules highlighting surface engineering of the core template nanomaterials (solid nanoparticles, liquid droplets, and gas bubbles) using chemicals or biomolecules which are able to direct nucleation and growth of silica at the boundary of two-phase interfaces (solid-liquid, liquid-liquid, and gas-liquid). Next, surface functionalization of silica nanocapsules is presented. Furthermore, strategies and challenges of encapsulating active molecules (pre-loading and post-loading approaches) in these capsular systems are critically discussed. Finally, applications of silica nanocapsules in controlled release, imaging, and theranostics are reviewed.