A microbial-mineralization-inspired approach directed the selective syntheses of copper oxides and related compounds from divalent copper ions in an aqueous solution at room temperature. The systematic syntheses were achieved by three routes; direct, transient-intermediate, and precursor-transformation routes. Inspired by microbial mineralization processes, the oxidation states, crystal phases, and morphologies of copper oxides and related compounds were controlled by the tuning of synthetic conditions. The present approaches facilitated the formation of spherical CuO and Cu2O crystals with hierarchical structures and high specific surface area. The resultant CuO hierarchical spheres showed improved properties as a catalyst for decomposition of an organic molecule in the presence of hydrogen peroxide.