A facile method to synthesize stable calcium carbonate microstructures is demonstrated which allows in situ encapsulation of sensitive molecules like drugs. The methodology involves a macromolecular assembly of anionic polypeptide with cationic peptide oligomer to concurrently template and hold to stabilize the mineralized structure. The heterogeneously distributed mixture of anionic and cationic residues in the macromolecular assembly, similar to that is found in natural systems assists in recognizing and coassembling Ca2+ and CO32− ionic clusters, especially for formation of a disordered precursor phase such as amorphous calcium carbonate (ACC) and further crystallization to form a metastable vaterite phase. The assembly also facilitates encapsulation of a guest molecule such as tetracycline at ambient conditions without affecting the mineralization process. The tetracycline-loaded microstructures show excellent antibacterial activities against many Gram-positive and Gram-negative bacterial strains and hence together with the fluorescence property of tetracycline and appropriate drug release profile, they can be used as multifunctional materials for therapeutic and imaging applications.