A sustainable and flexible approach for the extraction and separation of rhenium and molybdate species based on a polymeric aqueous two-phase system (ATPS) is proposed in which the high metal content in concentrated copper effluents is directly used as the driver of phase demixing. The partition coefficient and selectivity of Re, Mo, and Cu are studied in the proposed polymer-CuSO 4 -H 2 O ATPS as a function of additive concentration and polymer hydrophobicity. The electrolyte selection and concentration have a marked influence on the partition of Mo to the polymer phase, while increasing the hydrophobicity of the polymeric agent significantly improves the extraction of Mo. A selective precipitation based on the addition of quaternary ammonium salts directly to the polymer-rich phase is subsequently used for the quantitative recovery of Mo. A final polyoxometallate [N 2222 ] 2 Mo 6 O 19 hybrid complex is obtained with high purity. The resulting process achieves high separation yields, relies exclusively on cheap chemicals with low toxicity and could be a more sustainable alternative for the extraction of Re and Mo from copper mine effluents. By using sulfate salts as the salting-out agent, the main component of the ore leachate drives the separation thereby avoiding the use of additional complexing agents.