Microorganisms contribute to metal mobilization by catalyzing the dissolution of diverse compounds in both acidic and circumneutral environments. Since Mn(II) is more soluble than Mn(IV), acidophilic iron-reducing microorganisms, such as Acidiphilium cryptum, may increase the manganese contained in acid mine drainage from both active and abandoned mines. Two low-grade manganese ores (7% and 25% Mn) were used to perform dissolution tests with A. cryptum JF-5 in medium amended with oxalic acid, dissolved iron and thionine. The statistical analysis performed with a 99% confidence level demonstrated that the presence of Acidiphilium cryptum was the most important factor for manganese dissolution, increasing the process rate up to sevenfold (from 23.2 to 175.8 nmol/L·d). Pareto charts showed that the oxalate alone and the interaction of bacteria-Fe(II)-oxalate were also relevant in the dissolution process. The sulfuric acid used for pH control was proportional to the extracted amounts of manganese and iron, obtaining a consumption of 1.3 mol of H2SO4 per mol of metal. In the presence of A. cryptum, oxalic acid led to the selective dissolution of manganese, while thionine increased the dissolution of iron and decreased the process selectivity. Deoxygenation of the culture medium limited the bacteria proliferation and dissolution processes. Although the mechanism used by A. cryptum to dissolve both ores was not identified, the synthesis of bacterial appendages, or an iron- (or iron-chelate) mediated process may be essential when performing manganese dissolution.