Crude proteases extracted from papaya (Carica papaya) and pineapple (Ananas comosus) was obtained and studied for its utilization in making cottage cheese. Rennet was used to make cottage cheese control. The crude papaya protease was extracted from the latex of unripe green papaya skin. 1.14 gram of latex/1,000 gram of papaya was obtained. Crude pineapple protease was obtained by centrifuging juice of the pineapple at 4oC, 6,000 rpm for 10 minutes. 1,016 ml of supernatant/1,000 g pineapple flesh was obtained. The three proteases were analyzed for its specific activity by using Bergmeyer assay at pH 7 and temperature 32oC. Crude pineapple protease show the highest specific activity at 0.59 unit/g enzyme. The cottage cheese was made using the intended concentration of these proteases. Source of protease gave significant difference to the yield, bitter aftertaste, grainy texture, overall acceptance and texture of the cheese. The interaction between source of protease and concentration of protease gave significant difference to the protein content, ash content, carbohydrate content, whiteness index and yellowness index of the cheese. When compared with crude papaya protease, crude pineapple protease resulted in higher degree of undesirable sensory properties, such as bitterness, texture and overall acceptance. Concentration of the protease did not give any significant effect in term of sensory properties.