Aqueous two-phase systems (ATPS) are efficient, environmentally friendly, and “biocompatible” separation processes, which allow the recovery of enzymes. The most common systems are based on polymers and salts, and recently, to overcome the low polarity difference between the phases of the polymeric systems, ATPS based on ionic liquids (ILs) were proposed and have been successfully applied in this field. This work discusses the use of imidazolium-based ILs not as phase forming compounds but as adjuvants (5 wt%) in ATPS of polyethylene glycol systems (1500, 4000, 6000 and 8000 g mol⁻¹) with potassium phosphate buffer at pH 7, in the extraction and purification of a lipase produced by submerged fermentation by Bacillus sp. ITP-001. An initial optimization study was carried out with the commercial lipase B from Candida antarctica (CaLB) allowing us to further purify the commercial CaLB (purification factor = 5.2). Using the optimized conditions, a purification factor of 245 for the lipase from Bacillus sp. ITP-001 was achieved with 1-hexyl-3-methyl imidazolium chloride. The high purification factor is a consequence of the favorable interactions between the IL and the contaminant proteins that migrate for the PEG-rich phase, where the IL also concentrates preferentially, while the enzyme remains in the salt-rich phase.