Synergistically combining the merits of silica (e.g., mechanical robustness, biocompatibility and great versatility in surface functionalization) and capsular configurations (e.g., a large inner cavity, low density and favourable colloidal properties), silica-based nanocapsules (SNCs) with a size cutoff of ∼100 nm have gained growing interest in encapsulating bioactive molecules for bioimaging and controlled delivery applications. Within this context, this review provides a comprehensive overview of the synthetic strategies, structural control and biomedical applications of SNCs. Special emphasis is placed on size control at the nanoscale and material composition manipulation of each strategy and the newly emerging synthetic strategies. The applications of SNCs in bioimaging/diagnosis and drug delivery/therapy and the structure engineering that is critically important for the bio-performance of SNCs are also addressed in this review.