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There has been significant interest in ionic liquid aqueous two-phase systems (ILATPSs) with properties such as rapid phase segregation which can lead to a reduction in time taken for protein recovery. Evaluations of ILATPSs were performed with various types of ionic liquid ((Emim)BF4, (Emim)Br, (Bmim)BF4, and (Bmim)Br) and salts (potassium-, sodium-, and magnesium-based) as phase components to figure out their competencies in the recovery of lipase from a fermentation broth of E. coli using banana waste as a substrate. The results of this study revealed that an ILATPS comprising (Emim)Br/potassium phosphate significantly enhanced lipase recovery upon partitioning lipase. Optimization of the composition of the ILATPS using response surface methodology (RSM) significantly improved the purification factor (PF) and partition coefficient (Ke). The influences of crude loading (CL), pH changes, and the presence of NaCl on the recovery performance were also studied. Recovery of E. coli BL21 lipase was accomplished in an (Emim)Br/potassium phosphate ILATPS using 26.5% (w/w) (Emim)Br, 19% (w/w) potassium phosphate at pH 7.6, 3% NaCl and a crude loading of 7% (w/w). Using this ILATPS, lipase was successfully recovered in a single purification step, which gave a yield, PF and Ke of 93.75%, 3.394 and 1.352, respectively. A high PF value indicates that (Emim)Br/potassium phosphate is capable of attaining an excellent degree of lipase purity, suggesting that the proposed ILATPS is suitable for implementation in a large scale process for lipase purification.