The dietary proteins are one of the most important factors determining health conditions in human. The sufficient digestion and absorption of dietary proteins in the digestive tract have positive effects on performance and recovery in sportspeople or athletes. Improving of protein digestibility is a strategy for maintaining health status and optimal performance in sport or exercise activities. The hypothesis of the present study is that Weizmannia coagulans BC 99 (BC99) can increase muscle mass and strength. This randomized double-blind, controlled trial assigned 72 male college students to receive probiotics (n = 36, 20.25±1.03 years; 1.79±5.94 cm; 73.55±8.73 kg, protein powder with BC99) or placebo (n = 36, 20.19±0.79 years; 179.25±5.16 cm; 73.61±8.24 kg, protein powder) for 12-week. At the baseline and final stages of the study, strength tests and body composition assessment were performed; Blood and stool samples were taken at the end of the 12-week intervention, digestive enzymatic activity of stool samples, biochemical parameters, amino acids and hormone level of plasma were analyzed. BC99 administration significantly improved strength performance, skeletal muscle mass, activity of pepsin and trypsin, the concentrations of branched chain amino acids and essential amino acids, reduced activities of creatine kinase and lactic dehydrogenase and urea nitrogen (BUN) level, and increased testosterone and glucagon-like peptide-1 level in male college students. Therefore, BC99 supplementation can be an important nutritional strategy to improve strength performance, body composition, protein digestion and body metabolism in various groups of individuals.