Soil carbonates (inorganic C mainly as CaCO3) account for about 750 Gt C in the top 1 m and more than 2300 Gt in the top 2 m (nearly equal to organic C stocks). These inorganic C stocks have millennial to million-year turnover times and protect natural soils from degradation. Under croplands, however, these inorganic C stocks are continuously lost as CO2 by neutralization of N-fertilization-induced soil acidification. We estimated that over the last 50 years, at least 0.41 Gt C have been released irrecoverably as CO2 to the atmosphere from agricultural soils, and an additional 0.72 Gt C will be released until 2050. These inorganic C losses make our soils vulnerable to physical, chemical and biological degradation. Liming – a common agricultural practice to neutralize soil acidification – is the 2nd enormous source of irrecoverable C, accounting annually for 0.27 Gt C losses as CO2. In conclusion, soil carbonate loss due to N-fertilization-induced acidification is a huge source of unaccounted CO2 from C stock, which is irrecoverable over the mankind lifetime. © 2020 Elsevier B.V.