Recent studies carried out in coral reef settings or under controlled conditions showed that rising aqueous pCO2 (pH ≥ 7.8 – 7.9, and a saturation state of carbonate minerals > 1) stimulates the growth of reef microboring or euendolithic phototrophs, especially microalgae, and therefore, enhance rates of biogenic dissolution of carbonates. Those micro-organisms play a major role in reef bioerosion and coral reef functioning. In temperate-cold carbonate ecosystems, carbonate dissolution by euendolithic microflora has never been investigated under natural ocean acidification conditions. We thus realized two experiments to investigate the effects of low pH (and saturation states) on early natural microboring communities colonizing various carbonates and their associated rates of biogenic dissolution. One was carried out at Ischia (Italy) with mollusk shells exposed at two CO2 vents (pH < 7.5) vs an ambient site (pH ~ 8) during six months. The other one was realized at Faial (Azores) with various carbonate substrates (both aragonite and calcite) at one CO2 vent (pH ~ 7.4) vs an ambient site (pH ~ 8) over 45 days. Here we provide the data which allowed calculating rates of carbonate biogenic dissolution at all studied sites; i.e. the depth of penetration of euendolithic filaments into carbonates and the % of surface area of substrate colonized by microborers (bioeroded surface area). Rates of biogenic dissolution per site and per location are also provided, as well as environmental data collected at Faial (those collected at Ischia are published elsewhere). A total of 5 excel files is thus provided.