Cucumisin (CUC) from industrial melon by-products was separated for the first time through biological precipitation using carrageenan (CRG). This approach could represent a cost-effective and environmentally friendly process for the industries, avoiding the use of expensive equipment and toxic salts or solvents, such as butanol and ethanol. In this study, biological precipitation of proteins from melon by-products using CRG was studied and compared with conventional precipitation with ammonium sulphate. Different methods were applied for the identification and characterization of isolated proteins, including SDS-PAGE gel, FPLC and proteolytic activity assays. The isolated CUC confirmed a molecular weight of 68 kDa and showed highly stable proteolytic (PA) and milk-clotting (MCA) activities in a wide range of CaCl 2 (20-60 mM), pH (5-7) and temperatures (30-85 • C). Melon peel extract demonstrated to possess significant PA (4.24 U/mg protein) and MCA (191.50 MCU/mg protein), but such values were increased by ammonium sulphate precipitation (1.60 and 2.06-folds, respectively), and specially a noticeable increment was observed by biological precipitation with 2.11 and 17.65-folds, respectively, demonstrating the capability to be an effective strategy to isolate and purify CUC, allowing a yield of 0.17 g CUC/100 g of by-products and keeping its biological properties.