In order to recover biomolecules, a single downstream processing step is carried out. In this sense, an aqueous two-phase system (ATPS) containing polyethylene glycol (PEG) and potassium phosphate salts is used. Intending the purification of Burkholderia cepacia (Bc) lipase, the effects of the molecular masses of 1500 (PEG 1500), 4000 (PEG 4000), and 6000 (PEG 6000), pH (6, 7, and 8) and distinct tie line lengths are perfomed. Although this is reasonable reported in literature, a study covering an economical production aspect considering the Bc is scarce. This characterizes a novelty proposed in this investigation. Lipase is recovered in a polymer phase at lower pH value. PEG 1500/phosphate salt ATPS at pH 6 is considered a good method with similar to 98% of the extraction efficiency. Another contribution of this proposed investigation concerns to a biotechnological material synthesis, which is applied in several advanced and revolutionize engineering practices. Additionally, an economic analysis of the proposed method indicates a minimal sale price (similar to US$410/L) inducing to a future and potential commercial application.