The aim of this work was to produce bone scaffolds containing whey protein isolate and pearl powder and to conduct a preliminary assessment of the biomedical potential in vitro and in vivo. This included analysis of structural, physicochemical, mechanical, and biological properties, which revealed that biomaterials containing pearl powder exhibited an enhanced porous structure, increasing absorptive properties, and decreasing proteolytic capacity with increasing inorganic component content. Pearl powder content in the biomaterials did not clearly influence their mechanical properties or their ability to release calcium ions, as well as proteins. Extracts obtained from all tested biomaterials showed no cytotoxicity in vitro. The surfaces of all biomaterials promoted normal human osteoblast growth, proliferation, and osteogenic differentiation. Furthermore, all biomaterials did not display toxicity in vivo, but no changes in Danio rerio were observed after evaluation of the biomaterial containing the highest amount of pearl powder–10% v/w (marked as WPI/P10). Taking all the obtained results into account, it appears that this biomaterial can be promising for bone scaffolds and similar applications, thanks to its porous structure, high cytocompatibility in vitro, and lack of toxicity in vivo. However, advanced studies will be conducted in the future.