The factors influencing metal partition in acidic aqueous biphasic systems (AcABS) containing phosphonium-based ILs are still poorly explored. To assess their influence, the effect of the IL counter anion, acid and its concentration, and temperature, were systematically evaluated on the extraction of four transition metals (Cu(II), Co(II), Ni(II), and Mn(II)) and the lanthanide Ce(IV). The AcABS based on HCl showed good ability to extract Co(II) and Cu(II) to the IL-rich phase. In contrast, AcABS based on H2SO4 showed overall poor metal extraction, except for the [P44414]Cl + H2SO4 + H2O system. The latter showed good Cu(II) affinity at higher H2SO4 concentrations. The biphasic systems based on HNO3 were unable to extract transition metals to the IL-rich phase, with chloride from [P44414]Cl hampering Ce(IV) extraction. The [P44414]Cl + H2SO4 + H2O system was further optimized by adding small amounts of HCl to the system. The extraction efficiency of the metals is linked to the charge density of the metal-complex and its inherent free energy of hydration, the anion/water molar ratio changes induced by temperature and ionic strength, and the dissociation degree of the acid. By using these parameters it was possible to tune the selectivity and efficiency of the AcABS. Moreover, metal extraction was found to preferentially occur via an ion-pair mechanism, with split anion extraction taking place in AcABS containing different anions.