Plant phenolic compounds are known to interact with proteins producing changes in the food (e.g., biological value (BV), color, taste). Therefore, the in vivo relevance, especially, of covalent phenol-protein reactions on protein quality was studied in a rat bioassay. The rats were fed protein derivatives at a 10% protein level. Soy proteins were derivatized with chlorogenic acid and quercetin (derivatization levels: 0.056 and 0.28 mmol phenolic compound/gram protein). Analysis of nitrogen in diets, urine, and fecal samples as well as the distribution of amino acids were determined. Depending on the degree of derivatization, the rats fed with soy-protein derivatives showed an increased excretion of fecal and urinary nitrogen. As a result, true nitrogen digestibility, BV, and net protein utilization were adversely affected. Protein digestibility corrected amino acid score was decreased for lysine, tryptophan, and sulfur containing amino acids.