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Extracellular polymeric substances (EPS) secreted by rhizobacteria are ubiquitous in the environment and can enhance the negative charge of variable‐charge soils. Soil negative charge is directly related to pH buffering capacity (pHBC); it is essential to examine the effect of EPS on soil acidity and pHBC. We investigated the effect of adsorbed EPS on the acidification of five variable‐charge soils in China, which were subjected to different land use: an Oxisol and four Ultisols. Spectroscopic analysis revealed that EPS was specifically adsorbed onto soil surfaces through iron–oxygen–phosphorus/aluminum–oxygen–phosphorus (Fe‐O‐P/Al‐O‐P) bonds formed between phosphoryl groups of EPS and soil Al/Fe oxides. During the formation of Fe‐O‐P/Al‐O‐P bonds, there was ligand exchange between the EPS phosphoryl groups and the surface hydroxyl groups of Fe/Al oxides of the soils. The released OH– played an important role in soil acidity amelioration by the adsorbed EPS through neutralizing H+ and increasing soil suspension pH. After acidification, the pH of EPS‐treated soils was higher than that of the controls. This was attributed to a combined effect of enhanced soil pHBC, and protonation of organic anions (e.g., COO– to COOH) of EPS to decrease the activity of protons. The adsorbed EPS ameliorated prior soil acidity, inhibited new soil acidification, and promoted hydrolysis and re‐adsorption of Al. This was evident as the proportion of organically bound Al and adsorbed hydroxyl Al increased, whereas that of exchangeable Al decreased after EPS adsorption. Therefore, this study can serve as a reference for the molecular design of cost‐effective and environmentally friendly amendments for acid soils. Core Ideas: Variable charge soils can adsorb extracellular polymeric substances (EPS).Binding of EPS phosphoryl groups with soil Fe/Al oxides in soil released OH−.The released OH− from EPS adsorption increased soil pH and ameliorated soil acidity.Adsorbed EPS increased soil pH buffering capacity and inhibited soil acidification.EPS enhanced transformation of soil exchangeable Al to inactive solid Al in acid soils. [ABSTRACT FROM AUTHOR]