The sustainable extraction of manganese (Mn), a critical element used in many high-tech industries, has attracted considerable attention. However, the complex mineral composition makes the processing of manganese oxide ores challenging. This has led to an interest in green chemistry and alternative solvents to reduce environmental impacts. Deep Eutectic Solvents (DES) are recognized for their unique characteristics and environmental benefits. In this study, various DES comprising choline chloride as a hydrogen-bond acceptor (HBA) and organic acids such as oxalic acid (OX), tartaric acid (TA), and lactic acid (LA) as hydrogen-bond donors (HBDs) were synthesized. The key parameters, including HBA:HBD molar ratios, particle size, agitation speed, time, pulp density, and temperature, were systematically studied to optimize manganese recovery. By optimizing the parameters, 99.5% manganese extraction was achieved under the conditions of 40 g/L solid pulp, a molar ratio of 1:2, stirring speed of 200 rpm, temperature of 50 °C, and a leaching time of 1 h using ChCl:OX. Moreover, Density functional theory (DFT) was applied to evaluate the stability of various geometry-optimized Mn2+ complexes with the existing ligands such as OX, LA, TA, and Cl ion, by calculating the Gibbs free energy (ΔG(complex)) for each complex. The theoretical outcomes showed agreement with experimental results. DFT assessment revealed that Mn(OX)₂ has the most negative ΔG(complex) among the DES containing organic acid, followed by tartaric and lactic acid systems, indicating its potential for forming stable complexes with Mn2+. These findings highlight the potential of DES in efficient Mn recovery and simplify the traditional two-step pyro-hydro process by combining it into one step.