The characteristic shapes, structures and properties of biominerals arise from their interplay with a macromolecular matrix1, 2. The developing mineral interacts with acidic macromolecules, which are either dissolved in the crystallization medium or associated with insoluble matrix polymers3, that affect growth habits and phase selection or completely inhibit precipitation in solution4, 5, 6. Yet little is known about the role of matrix-immobilized acidic macromolecules in directing mineralization. Here, by using in situ liquid-phase electron microscopy to visualize the nucleation and growth of ¿CaCO3 in a matrix of polystyrene sulphonate (PSS), we show that the binding of calcium ions to form Ca–PSS globules is a key step in the formation of metastable amorphous ¿calcium carbonate (ACC), an important precursor phase in many biomineralization systems7. Our findings demonstrate that ion binding can play a significant role in directing nucleation, independently of any control over the free-energy barrier to nucleation.