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Modified Dried Skimmed Milk Coconut Oil (Modisco) III formulation is a high protein liquid food for severe malnutrition nutrition therapy in phase III (rehabilitation phase). Soybean is well-known as one of the foods that contains high protein with complete amino acids. This research was conducted in order to analyze the quality of protein of Modisco III formulation addition with soybean flour. The true experiment design of randomized pre test-post test control group for 24 Wistar rats male that had been made into severe malnutrition condition. There were divided into 4 group: group 1 was treated with standard food (AIN-93), whereas group 2, 3, 4 were treated with low protein food (cassava-based food). After getting severe malnutrition, group 3 was given Modisco III Formulation with 25% soybean flour addition and group 4 was given combination of Modisco III Formulation with 25% soybean flour addition (80% of total daily food) and cassava-based food (20% of total daily food). Protein Efficiency Rate (PER) was used to analyze protein quality. Data was analyzed with Mann Whitney and Kruskall Wallis test with 0,05 significant level. The result showed that PER each group were 1,78+0,01 (Group 1), 0,88+0,08 (Group 2), 1,47+0,04 (Group 3), and 0,33 + 0,02 (Group 4), respectively. There were differences between group significanly (p=0,0001), and group 3 had the closest PER with group 1. Soybean flour might able to being altenative high protein ingredient for Modisco formulation to improve nutrition status.