Biominerals provide excellent mechanical properties for skeletal support and protection, rivaling and even outperforming those of many engineered ceramics fabricated at high temperatures and pressures. However, the mechanisms of biomineralization are still poorly understood. To make progress in this direction, here we study the crystallization of calcite (thermodynamically the most stable CaCO3 phase) from an amorphous calcium carbonate (ACC) precursor inside a three-dimensional insoluble chitosan scaffold. A hydrated ACC phase with complete disorder is found to first nucleate from citrate–calcium ion pairs and subsequently transform into stabilized ACC nanoparticles with a short-range order of calcite, which then crystallize and grow into calcite nanocrystals via the transient ACC phase, instead of direct crystallization from the hydrated ACC precursor as reported previously. The calcite nanocrystals are aggregated and collectively oriented into rough rhombohedral calcite mesocrystals, and eventually evolve into smooth mesocrystals. Mechanical property characterizations of the novel bio-inspired nanocomposites show a strong dependence on the content of the constituent inorganic nanocrystals. Furthermore, the reduced elastic modulus is closely related to the interfacial interaction strength between the inorganic nanocrystals and the organic matrix, whereas the hardness is dependent on the crystallinity of the constituent inorganic mesocrystals in the nanocomposites.