AbstractMicrobial‐induced calcite precipitation (MICP) is regarded as environmentally friendly, partly due to the storage of carbon as carbonates. Although CO2 emissions during MICP have been reported, quantification of its environmental impact regarding total greenhouse gas fluxes has not yet been thoroughly investigated. In particular, N2O fluxes could occur in addition to CO2 since MICP involves the microbially mediated nitrogen cycle. This study investigated the greenhouse gas fluxes during biostimulation of MICP in quartz sand in incubation experiments. Soil samples were treated with MICP cementation solution containing calcium concentrations of 0, 20, 100 and 200 mM at a fixed urea concentration of 100 mM to offer a range of carbonation potential and/or mitigation of CO2 emissions. Greenhouse gas (CO2, CH4 and N2O) measurements were determined by gas chromatography during incubations. Soil total inorganic carbon and the isotopic composition of precipitated and emitted CO2 were determined by isotope ratio mass spectrometry. CO2 emissions (0.52 to 4.08 μg of CO2–C h−1 g−1 soil) resulted from MICP, while N2O and CH4 fluxes were not detected. Increasing Ca2+ with respect to urea resulted in lower CO2 emissions, lower solution pH, similar carbonate precipitation and urea hydrolysis inhibition. The highest urea‐to‐calcium ratio (1:0.2) emitted roughly two times the amount of CO2 (112 μg of CO2–C g−1 soil) compared to the 1:1 and 1:2 ratios (47 to 58 μg of CO2–C g−1 soil) and five to six times more than samples that did not receive Ca2+ (1:0) (~18 μg of CO2–C g−1 soil). Precipitated CaCO3–C was tenfold higher than cumulative emitted CO2–C, and isotopic analysis indicated both emitted and precipitated carbon were of urea origin. Both emitted and precipitated carbon accounted for a very low percentage of total carbon applied in the system (<0.35 and <4.5%, respectively), presumably due to limited urea hydrolysis which was negatively affected by increasing the Ca2+ concentration.