A successful process to extract lipolytic enzymes based on an aqueous biphasic system (ABS), which uses both ionic liquids (ILs) and a high charge-density inorganic salt (K2CO3), is proposed in this work. The activity of a model Thermomyces lanuginosus lipase (TlL) in some of the most common hydrophilic ILs, based on the 1-alkyl-3-methylimidazolium cation, combined with chloride, alkylsulfate, alkylsulfonate and acetate, was investigated. Several operating conditions influencing lipase activity and ABS formation were investigated. Parameters such as temperature, pH, deactivation kinetics and water content were evaluated in order to propose a viable extraction process. A deeper analysis in terms of enzyme deactivation kinetics was carried out, and the data were modelled through a series-type deactivation equation. ATR-FTIR studies aimed at identifying the TlL structure in selected ILs have also provided an insight into the enzyme deactivation behaviour.