The synthesis of ultrafine, uniform, well-dispersed functional nanoparticles (NPs) under mild conditions in a controlled manner remains a great challenge. In biological systems, a well-defined biomineralization process is exploited, in which the control over NPs' size, shape and distribution is temporally and spatially regulated by a variety of biomolecules in a confined space. Inspired by this, we embedded proteins into metal-organic frameworks (MOFs) and explored a novel approach to synthesize metallic NPs by taking the synergy of protein-induced biomineralization process and space-confined effect of MOFs. The generation and growth of ultrafine metal NPs (Ag or Au) was induced by the entrapped lysozyme molecules and confined by the ZIF-8 pores. Due to the narrow size distribution and homogeneous spatial distribution of metal NPs, the as-synthesized NPs exhibit remarkably elevated catalytic activity. These findings demonstrate that MOFs can be loaded with specific proteins to selectively deposit inorganic NPs via biomimetic mineralization and these novel kinds of nanohybrid materials may find applications in catalysis, sensing and optics.