The era of electric vehicles is rapidly approaching, and therefore, it is crucial to provide a sustainable technology for ensuring the circular economy of lithium-ion batteries. In this study, we report the development of a novel aqueous biphasic system (ABS) comprising fully biocompatible components, that is, hydrophilic ionic liquids, amino acids, and organic acids, for the selective recovery of Co(II) and Ni(II) from Mn(II), which are critical metals in spent lithium-ion batteries. Separation of Co(II), Ni(II), and Mn(II) from sulfate media was successfully carried out using the ABS in a quite straightforward manner without any hazardous reagents or organic solvents. In addition, the plausible mechanism of metal ion separation within the ABS was elucidated. The regenerated ionic liquid in the ABS exhibited remarkably stable performance during use in three consecutive experimental cycles.