Calcite crystals with a rhombohedral morphology were synthesized using a biomimetic method in the presence of organic structure-directing agents (chitosan and gum arabic). Analysis of the microstructures of these crystals by scanning electron microscopy, high resolution transmission electron microscopy and powder X-ray diffraction revealed a non-classical growth mechanism. Initially, the biomaterials and inorganic precursor molecules aggregated into large particles. Multiple nucleation of CaCO3 took place either on the surface of the aggregates (in the chitosan system) or inside the aggregates (in the gum arabic system). These nanocrystallites aggregated again to form some large polycrystalline rhombohedral or spherical particles. Surface recrystallization then occurred, forming small single-crystal islands, which joined together as the reaction time increased leading to a core–shell structure where a polycrystalline core was encased in a thin single-crystal shell. The crystallization then extended from the surface to the core, ultimately resulting in true single crystals.