Spent lithium-ion batteries have caused global concern owing to their rich resource metal content and high potential for polluting the environment. In the present study, a green, efficient, and simple process was developed to recycle and detoxify Li, Mn, Cu, Al, Co, and Ni from spent lithium-ion mobile phone batteries using adapted Aspergillus niger. The adaptation of Aspergillus niger to heavy metals improved the production of organic acids and the leaching efficiency of metals compared to unadapted fungi. Moreover, it decreased the time required to enter the logarithmic phase and increased the speed of acid production. In the presence of spent lithium-ion battery powder, gluconic acid was the main lixiviant produced by the adapted fungi. At a pulp density of 1% (w/v), the adapted Aspergillus niger leached 100% Li, 94% Cu, 72% Mn, 62% Al, 45% Ni, and 38% Co. The results of SEM, FTIR, XRD, EDX, and mapping analyses of the original spent battery powder and bioleached residue confirmed the effectiveness of fungal metabolites to leach the metals of spent lithium-ion mobile phone batteries.