Pectinase activity by Aspergillus flavipes was increased when scaled-up from 1 to 5 L. Logistic, Gompertz and Luedeking & Piret models were used to characterize the process. Cholinium-based ionic liquids are suitable extraction agents in tergitol solutions. Ionic liquid-based Aqueous Biphasic Systems led to 90% of pectinase extraction.