Rising atmospheric CO2 is acidifying the world’s oceans, afecting both calcifcation and dissolution processes in coral reefs. Among processes, carbonate dissolution by bioeroding microflora has been overlooked, and especially its impact on seawater alkalinity. To date, this biogeological process has only been studied using microscopy or buoyant weight techniques. To better understand its possible efect on seawater alkalinity, and thus on reef carbonate budget, an experiment was conducted under various seawater chemistry conditions (2≤Ωarag≤3.5 corresponding to 440≤pCO2 (μatm)≤940) at 25 °C under night and daylight (200 μmol photons m−2 s−1) with natural microboring communities colonizing dead coral blocks (New Caledonia). Both the alkalinity anomaly technique and microscopy methods were used to study the activity of those communities dominated by the chlorophyte Ostreobium sp. Results show that (1) the amount of alkalinity released in seawater by such communities is signifcant and varies between 12.8±0.7 at ΩArag~2 and 5.6±0.4 mmol CaCO3 m−2 day−1 at ΩArag~3–3.5 considering a 12:12 photoperiod; (2) although dissolution is higher at night (~ 80 vs. 20% during daylight), the process can occur under signifcant photosynthetic activity; and (3) the process is greatly stimulated when an acidity threshold is reached (pCO2≥920 μatm vs. current conditions at constant light intensity). We show that carbonate dissolution by microborers is a major biogeochemical process that could dissolve a large part of the carbonates deposited by calcifying organisms under ocean acidifcation.