The construction of organic-inorganic hybrid materials has shown great potential for the development of multifunctional superior protein-based composites. However, it is still a challenge to effectively disperse and dominate the mineralization of inorganic minerals in a hybrid system. In this study, we presented a simple and green strategy to construct a biomineralized soy protein (SP)-based hybrid resin with a controllable mineralized skeleton. It was found that the Pickering emulsion served as a mineralized template efficiently inducing the uniform dispersion of inorganic particles while the incorporated cellulose nanocrystals (CNC) were able to regulate the mineralization process, thus forming an optimized mineralized skeleton structure. Acting as a reactive reinforcer, the regulated mineralized skeleton formed in situ interactions with SP matrix, giving rise to the multiple covalent and ionic crosslinking networks. As a result, the introduction of mineralized skeleton increased the wet shear strength of composites from 0.46 MPa to 1.21 MPa, exhibiting a 163% increment compared to the pristine SP composite. Moreover, the formation of rigid inorganic mineralized skeleton in hybrid SP-based resin facilitated an obvious improvement of thermal stability compared with the control samples. Overall, we envisage that this strategy could provide a creative strategy for the design and fabrication of superior sustainable bio-composites for engineered wood products.