Compositing complementary flours with legumes of high protein quality such as soy can be effective in abating Protein Energy Malnutrition. Soy-fortified complementary flours were developed using locally available foods from Western Kenya and used to determine the fortification effect on protein nutritional quality, growth, and rehabilitation. Ten isonitrogenous diets containing 10% protein and one containing 20% protein were formulated from six foods; maize, pearl millet, finger millet, sorghum, cassava, and banana at ratios of 70:30 flour and soy with milk powder as control and fed to weanling male albino rats. Another group was fed on a protein free diet. Banana: Soy diet had significantly superior protein nutritional quality while Maize: soy had 70% Protein Digestibility Corrected Amino Acid Score. True Protein Digestibility of the fortified diets lay within the acceptable margin for cereal: bean mixtures. Fortification with soy improved protein quality indices of flours in rats, and by extrapolation could support growth of young children if used as complementary foods.