Excessive application of mineral fertilizers has accelerated soil acidification in China, affecting crop production when the pH drops below a critical value. However, the contributions of natural soil acidification, induced by leaching of bicarbonate, and anthropogenic causes of soil acidification, induced by nitrogen (N) transformations and removal of base cations over acid anions, are not well quantified. In this study, we quantified soil acidification rates, in equivalents (eq) of acidity, by assessing the inputs and outputs of all major cations and anions, including calcium, magnesium, potassium, sodium, ammonium, nitrate, bicarbonate, sulphate, phosphate and chloride, for 13 long-term experimental sites in southern China. The acidification rates strongly varied among fertilizer treatments and with the addition of animal manure. Bicarbonate leaching was the dominant acid production process in calcareous soils (23 keq ha−1 yr−1) and in non-calcareous paddy soils (9.6 keq ha−1 yr−1), accounting for 80 % and 68 % of the total acid production rate, respectively. The calcareous soils were strongly buffered, and acidification led no or a limited decline in pH. In contrast, N transformations were the most important driver for soil acidification at one site with upland crops on a non-calcareous soil, accounting for 72 % of total acid production rate of 8.4 keq ha−1 yr−1. In this soil, the soil pH considerably decreased being accompanied by a substantial decline in exchangeable base cation. Reducing the N surplus decreased the acidification rate with 10 to 54 eq per kg N surplus with the lowest value occurring in paddy soils and the highest in the upland soil. The use of manure, containing base cations, partly mitigated the acidifying impact of N fertilizer inputs and crop removal, but enhanced phosphorus (P) accumulation. Combining mineral fertilizer, manure and lime in integrative management strategies can mitigate soil acidification and minimize N and P losses.