Quantifying the link between cyanobacterial activity and the carbon isotope signature of precipitated carbonate minerals is crucial for reconstructing the environmental conditions present at the time of carbonate mineral formation. In this study, calcite was precipitated in the presence and absence of Synechococcus sp. cyanobacteria in batch reactors. The temporal evolution of the carbon isotope composition of calcite (δ13CCalcite) and dissolved inorganic carbon (δ13CDIC) was monitored to evaluate the rate and degree to which the carbon isotope compositions in calcite are modified during and after its precipitation. The presence of cyanobacteria promoted calcium carbonate formation by increasing fluid pH and the CaCO3 saturation state. It also changed significantly the carbon isotope composition of dissolved inorganic carbon due to the preferential incorporation of 12C into the biomass. This generated an isotope disequilibrium between the calcite and the aqueous fluid phase over time after the calcite precipitated. The carbon isotope composition of the calcite evolved continuously towards mineral-fluid isotope equilibrium after its precipitation, at geometric surface area normalized rates ranging from 1.75 × 10−14 to 1.71 × 10−13 mol 13C/m2/s. These rates are sufficiently fast such that the δ13CDIC value of aqueous fluids in calcite-rich rocks would be buffered by the δ13CCalcite value of the co-existing calcite. Mass balance calculations suggest that the carbon isotope composition of calcite could change noticeably when the calcite is in isotope disequilibrium with its co-existing fluid, for example through the presence of a local 12C sink such as photosynthetic microorganisms or 12C source such as decomposition of organic material.