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Soil acidification has been a serious problem in abandoned mine areas, and could be exacerbated by acid deposition with the release of mine wastes. In this study, three different indigenous bacterial consortia were isolated from abandoned mines in South Korea, from which the potential for acid neutralization of microorganisms was evaluated. They were all able to neutralize acidity within 24 h in the liquid nutrient medium. Moreover, a strong positive correlation (R = +0.922, <i>p</i> < 0.05) was established between the ammonium ion (NH₄⁺) production yield and the resulting pH, indicating that NH₄⁺ served as an important metabolite for biological neutralization. <i>Serratia</i><i>liquefaciens</i>, <i>Citrobacter youngae</i>, <i>Pseudescherichia vulneris</i>, and <i>Serratia grimesii</i> had higher acid neutralization ability to generate NH₄⁺ by the metabolism of nitrogen compounds such as carboxylation and urea hydrolysis. Therefore, acidic soils can be expected to be ameliorated by indigenous microorganisms through in situ biostimulation with the adequate introduction of nitrogenous substances into the soil environments.