Bioinspired synthesis of silica has attracted attention from a wide range of researchers as novel route for fabrication of various nanomaterials. Proteins including silaffins and silicateins as well as polyamines from marine diatoms and sponges are key biomolecules in these biomimetic silicification processes. These methods allow silica mineralization from various silica precursors under mild, biologically compatible conditions in an unprecedentedly fast and facile manner. Notably, the silica polycondensation entails the concomitant encapsulation of other molecules in the reaction solutions. Due to the efficient encapsulation and synergetic effects brought by the encapsulated molecules and the characteristics of biomimetic silica synthesis as well as the mechanical and chemical properties of silica itself, the silica-biomolecule nanocomposites have broad applications in biocatalysis, biosensor, and biomedical areas. Introduction and combination of novel template, precursors, inorganics, or enzymes with the previously used strategies will allow construction of more efficient, purpose-optimized silica nanomaterials with controlled size, composition, and morphology.