A multifunctional nanostructured hybrid composed of metal–protein–ceramic was designed and then synthesized using three different methods: chemical reduction, physical adsorption, and coprecipitation. The processes yielded colloidal spherical silver nanoparticles (AgNPs) enveloped in a bovine serum albumin (BSA) corona, leading to the core–shell structure AgNPs–BSA. To enhance biocompatibility and mitigate potential toxicity associated with metallic nanoparticles, this core–shell structure was coated with a layer of calcium carbonate (CaCO3). In order to analyze the internal structure of the resulting hybrid nanostructure (AgNPs–BSA–CaCO3), a number of samples were produced by focused ion beam (FIB) and characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), atomic force microscopy (AFM), X‐ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, and zeta potential (ζ) measurements. The cytotoxic effect of the samples were evaluated through in vitro tests on mouse macrophage cell line RAW 264.7 ATCC TIB‐71, this was accomplished by calculating the appropriate concentrations from the dose–response curve of AgNPs. Research showed that the AgNPs–BSA–CaCO3 mixture triggered the formation of vaterite; these findings were corroborated by FTIR and Raman techniques. The spherical nanostructures have an average diameter size of 4.3 ± 2 μm and an average roughness (Ra) of 3.11 ± 0.62 μm. Zeta potential (ζ) and isoelectric point studies reveal that this hybrid nanostructure exhibits amphoteric behavior that differs from either AgNPs or AgNPs–BSA alone. Cell viability response exceeded 75%, indicating the noncytotoxic nature of the proposed hybrid nanostructures.