Atmospheric acid deposition remains a widespread problem that may influence the protection of carbon (C) in soil by altering organo-mineral interactions. However, the impacts of additional acidity on organo-mineral interactions and soil C sequestration in naturally acidic tropical soils with a high content of reactive iron (Fe) phases have not been well studied. Here we sampled a nearly 10-yr field experiment with a gradient of acidity treatments (0, 9.6, 32, 96 mol H+ ha− 1 yr− 1 as nitric acid + sulfuric acid) to examine how acidification alters organo-mineral interactions and soil organic carbon (SOC) pools in a tropical forest in southern China. As expected, soil acidification significantly enhanced the leaching of base cations (e.g., Ca2+), and it also altered the solubility and composition of Fe and Al phases. The acidity treatments converted more crystalline Fe (oxyhydr)oxides to short-range-ordered phases, resulting in a large increase in Fe-bound C vs. a relatively small decrease in Ca-bound C. Overall, the acidity treatments increased the mineral-associated C stock to 32.5–36.4 Mg C ha− 1 vs. 28.8 Mg C ha− 1 in the control, accounting for 71–83% of the observed increase in total SOC stock. These findings highlight the importance of pH-sensitive geochemical changes and the key roles of Fe in regulating the response of SOC to further inputs of acid deposition even in highly weathered and naturally acidic soils. The magnitude of SOC changes observed here indicates the importance of including pH-sensitive geochemistry in Earth system models to predict ecosystem C budgets under future acid deposition scenarios.