Calcium carbonate (CaCO3) is one of the most abundant and important biominerals in nature. Due to its biocompatibility, biodegradability and nontoxicity, CaCO3 has been investigated extensively in recent years for various fundamental properties and technological applications. Inspired by basic wall structures of cells, we report a protein-assisted approach to synthesize CaCO3 into a double-shelled structural configuration. Due to varying reactivities of outer and inner shells, the CaCO3 microcapsules exhibit different sorption capacities and various resultant structures toward different kinds of heavy metal ions, analogical to biologically controlled mineralization (BCM) processes. Surprisingly, three mineralization modes resembling those found in BCM were found with these bacterium-like “CaCO3 cells”. Our investigation of the cytotoxicity (MTT assay protocol) also indicates that the CaCO3 microcapsules have almost no cytotoxicity against HepG2 cells, and they might be useful for future application of detoxifying heavy metal ions after further study.