We investigated calcium interactions with the surface of individual living cells of the freshwater cyanobacterium Synechococcus leopoliensis PCC 7942 under illumination and calcite supersaturation, with respect to calcium carbonate nucleation on the cell surface. Immobilized living cells were scanned by Atomic Force Microscopy (AFM) with conventional and chemically modified tips which were coated with carboxylic groups, so-called Chemical Force Microscopy (CFM). Calcium adsorption was heterogeneous and altered the surface charge of the cells. This was confirmed by bulk measurements of the zeta-potential at different Ca²⁺ concentrations and compared to measurements made with other bivalent cations (Mg²⁺, Sr²⁺, Ba²⁺). Zeta-potential increased rapidly (<2 min) from −46.9 mV in calcium-free solution to +0.8 mV in 22 mmol L⁻¹ CaCl₂ solution, using a 1.5 mmol L⁻¹ NaHCO₃ solution as background electrolyte in both cases. This was followed by the slow (several hours) formation of nonmineralized protuberances at the cell surface. These changes in the microtopography did not show obvious spatial relationship to surface charge or Ca²⁺ adsorption. The formation of the protuberances was reversible when Ca²⁺ was removed from the circumfluent solution. Ca²⁺ adsorption to the cell surface was faster than calcium-induced changes in the surface microtopography and much faster than calcite nucleation on the cell surface which was observed on a fraction of the cells in previous bulk experiments under similar supersaturation.