Proteins can control mineralization of CaCO3 by selectively triggering the growth of calcite, aragonite or vaterite phases. The templating of CaCO3 by proteins must occur predominantly at the protein/CaCO3 interface, yet molecular-level insights into the interface during active mineralization have been lacking. Here, we investigate the role of peptide folding and structural flexibility on the mineralization of CaCO3. We study two amphiphilic peptides based on glutamic acid and leucine with β-sheet and α-helical structures. Though both sequences lead to vaterite structures, the β-sheets yield free-standing vaterite nanosheet with superior stability and purity. Surface-spectroscopy and molecular dynamics simulations reveal that reciprocal structuring of calcium ions and peptides lead to the effective synthesis of vaterite by mimicry of the (001) crystal plane.