In this work, biocompatible ionic liquids based on aminoacids were employed as extractants to separate extremolipases from aqueous streams. First, the influence of aminoacid and dipeptide-based ionic liquids (cholinium glycinate, ChGly, and cholinium glycylglycinate, ChGlygly) on the lipolytic activity of a commercial lipase from Candida antarctica (CaLB) and in-house synthesized extremophilic lipases from Thermus thermophilus HB27 (TtHB27L) and Halomonas sp. LM1C (HL) was investigated. The combination of thermophilic enzyme with ChGly turned out to be the optimum combination for maximizing the biocatalytic performance, clearly improving the levels attained when water was exclusively employed as solvent and also surpassing the activity levels provided for the commercial enzyme CaLB. The salting out capacity of ChGly in aqueous solutions of biodegradable surfactants Tergitol 15S7 and Tergitol 15S9 was discussed, recording immiscibility areas almost covering all the ternary diagrams. The aqueous biphasic systems were experimentally characterized by determining both tie-lines and solubility curves at several temperatures and the data was modelled with relevant equations like Merchuk, Othmer-Tobias and Bancroft ones, as they are the most common ones to describe this kind of equilibrium data. So, ChGly was applied to extract thermophilic and commercial lipases from aqueous solutions at 313.15 K, achieving very high extraction levels (about 100 %) for TtHB27L, which clearly surpasses the maximum extraction values observed for the commercial enzyme (about 80 %). Finally, the process was simulated at real scale through SuperPro Designer v.8.5 for the production of 385 Kg/year of extremolipase.