Protein−inorganic hybrid nanoflowers (HNFs) possess unique properties in promoting surface reactions and have attracted wide-spread attention as a newly developed nanomaterial. However, the availability of protein sources has been mostly limited to enzymes, which narrows the application of HNFs. This study first investigated the HNF formation ability of soy protein, which shows poor performance in its native state. We show that treatment of the protein by enzymatical hydrolysis can significantly promote its ability to form HNFs, by enhancing its flexibility and mobility and increasing the nucleation sites of HNFs. The hydrolyzed soy protein also showed broad ability to form HNFs with many types of metal ions including Cu 2+ , Mn 2+ , Fe 2+ , and Ca 2+ indicated by both optical microscopy and scanning electron microscopy (SEM). Furthermore, the hydrolyzed soy protein-based HNFs display high encapsulation capacity of natural water-soluble Monascus red pigment (550 mg/(g HNF)) and oil-soluble curcumin pigment (21.9 mg/(g HNF)), while effectively improving the thermal stability and ultraviolet (UV) light stability of these pigments. Finally, 10 more food proteins were subjected to enzymatic hydrolysis, and all of them demonstrate pronounced improvement in their HNF formation ability. This research demonstrates that enzymatic hydrolysis is an effective tool for utilizing abundant food proteins to fabricate HNFs, and these food protein-based HNFs have high potential as novel delivery systems�especially for sensitive natural pigments�for food, cosmetic, and medicinal applications.