Abstract Soil carbon is major driver of climate in the long term because soil can either decrease global warming by carbon sequestration or increase warming by emissions of greenhouse gases. Soil inorganic carbon is mainly composed of carbonates and represents globally more than half of the total soil carbon stock up to a 2-m depth. The dissolution of carbonates by fertilization-induced acidification may offset the global efforts aimed at organic carbon sequestration, yet this process is poorly understood. Here, we evaluated the effects of fertilization strategies on inorganic carbon contents and stocks to 120 cm soil depth by using natural δ13C signature of organic and inorganic carbon in 32- and 40-year field experiments. Results show that long-term application of mineral nitrogen and phosphorous fertilizers acidified soils by 0.2 pH units. This caused inorganic carbon dissolution and carbon dioxide emissions of 9–12 Mg C per hectare, representing 12–18% of the initial stock in the top 60 cm. By contrast, manure application increased inorganic carbon stock by 8.9–11 Mg C per hectare, representing 4.8–17% of the initial stock up to 120 cm depth. The main pathway of inorganic carbon accumulation under organic fertilization is the neoformation of pedogenic carbonates and the conservation of lithogenic carbonates. Manure combined with mineral fertilizers did not affect inorganic carbon and therefore provides an optimal solution to mitigate carbon losses from soil.