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Serpentinite replacement by carbonates in the seafloor is one of the main carbonation processes in nature providing insights into the mechanisms of CO₂ sequestration; however, the onset of this process and the conditions for the reaction to occur are not yet fully understood. Preserved serpentine rim with pseudomorphs of carbonate after serpentine and lobate-shaped carbonate grains are key structural features for replacement of serpentinite by carbonates. Cathodoluminescence microscopy reveals that Ca-rich carbonate precipitation in serpentinite is associated with a sequential assimilation of Mn. Homogeneous δ¹⁸O values at the µm-scale within grains and host sample indicate low formation temperature (<20 °C) from carbonation initiation, with a high fluid to rock ratio. δ¹³C (1−3 ± 1‱) sit within the measured values for hydrothermal systems (−3−3‱), with no systematic correlation with the Mn content. δ¹³C values reflect the inorganic carbon dominance and the seawater source of CO₂ for carbonate. Thermodynamic modeling of fluid/rock interaction during seawater transport in serpentine predicts Ca-rich carbonate production, at the expense of serpentine, only at temperatures below 50 °C during seawater influx. Mg-rich carbonates can also be produced when using a model of fluid discharge, but at significantly higher temperatures (150 °C). This has major implications for the setting of carbonation in present-day and in fossil margins.