Nowadays ionic liquids (ILs), because of their “green” characteristics, have been used for analytical and separation processes. Therefore the partitioning of lysozyme and α-lactalbumin using aqueous two-phase systems (ATPSs) composed of an ionic liquid (chloride 1-ethyl-3-methylimidazolium) and inorganic salts (K2HPO4, KH2PO4) was studied. Phase equilibrium diagrams were obtained to explore the effect of the different temperatures (293.15, 303.15, 313.15, and 323.15) K and pH (7.5, 8.0, and 8.5) used for the partitioning studies. For both proteins, partition coefficients decreased with increasing temperature. The pH influenced the partition coefficients of lysozyme and α-lactalbumin. The thermodynamic parameters (ΔH◦, ΔS◦, ΔG◦) indicate thermodynamic differences between the partitioning of lysozyme and α-lactalbumin in this system. The ΔH◦, ΔS◦, and ΔG◦values of the process studied showed that this process is spontaneous. This work demonstrates the possible use of ATPSs with ILs and inorganic salts as a methodology for the partitioning of lysozyme and α-lactalbumin.