Biomineralization reactions provide an effective mechanism to generate inorganic matrices that are suitable for enzyme immobilization. A range of cationic proteins and polypeptides, for example, catalyze the biomineralization of silica in vitro; the biomolecules acting as a scaffold during the formation of the silica matrix. In general the silica precipitation reaction forms a network of fused spherical silica nanoparticles, although size and morphology is dependent upon the choice of catalyst and the reaction environment. When additional enzymes are added during the formation of silica, the enzymes become encapsulated within the silica particles as they form. The silica forms at ambient environmental conditions, providing mild encapsulation conditions and high biocompatibility to the encapsulated biomolecules. The versatility of the silica-immobilization method has been demonstrated for a variety of enzymes with consistently high immobilization efficiencies and retention of enzyme activity. The versatility of silica-encapsulated enzymes will be presented for a range of model applications including biocatalysis, development of biosensors and applications to biofuel cell design. In addition, lysozyme has recently been shown to act as a scaffold for silica formation. Lysozyme retains its anti-microbial properties when entrained within the resulting silica particles. Advances in the characterization and elucidation of these mechanisms in respect to the development of anti-microbial coatings will also be presented.