Photosynthetic uptake of inorganic carbon can raise the pH adjacent to cyanobacterial cells, promoting CaCO3 precipitation. This effect is enhanced by CO2 concentrating mechanisms that actively transport into cells for carbon fixation. CO2 concentrating mechanisms presumably developed in response to atmospheric decrease in CO2 and increase in O2 over geological timescales. In present-day cyanobacteria, CO2 concentrating mechanisms are induced when the atmospheric partial pressure of CO2 (pCO2) falls below ∼0.4%. Reduction in pCO2 during the Proterozoic may have had two successive effects on cyanobacterial calcification. First, fall in pCO2 below ∼1% (33 times present atmospheric level, PAL) resulted in lower dissolved inorganic carbon (DIC) concentrations that reduced pH buffering sufficiently for isolated CaCO3 crystals to begin to nucleate adjacent to cyanobacterial cells. As a result, blooms of planktic cyanobacteria induced precipitated ‘whitings’ of carbonate mud in the water column whose sedimentary accumulation began to dominate carbonate platforms ∼1400–1300 Ma. Second, fall in pCO2 below ∼0.4% (10 PAL) induced CO2-concentrating mechanisms that further increased pH rise adjacent to cells and promoted in vivo cyanobacterial sheath calcification. Crossing of this second threshold is indicated in the fossil record by the appearance of Girvanella 750–700 Ma. Coeval acquisition of CO2 concentrating mechanisms by planktic cyanobacteria further stimulated whiting production. These inferences, that pCO2 fell below ∼1%∼1400–1300 Ma and below ∼0.4% 750–700 Ma, are consistent with empirical and modelled palaeo-atmosphere estimates. Development of CO2 concentrating mechanisms was probably temporarily slowed by global cooling ∼700–570 Ma that favoured diffusive entry of CO2 into cells. Lower levels of temperature and DIC at this time would have reduced seawater carbonate saturation state, also hindering cyanobacterial calcification. It is suggested that as Earth emerged from ‘Snowball’ glaciations in the late Neoproterozoic, global warming and O2 rise reactivated the development of CO2 concentrating mechanisms. At the same time, rising levels of temperature, calcium ions and DIC increased seawater carbonate saturation state, stimulating widespread cyanobacterial in vivo sheath calcification in the Early Cambrian. This biocalcification event promoted rapid widespread development of calcified cyanobacterial reefs and transformed benthic microbial carbonate fabrics.