Background: The dietary proteins are one of the most important factors determining health conditions in humans. The sufficient digestion and absorption of dietary proteins in the digestive tract has positive effects on performance and recovery in sportspeople and athletes. Improving protein digestibility is a strategy for maintaining health status and optimal performance in sport and exercise activities. Objectives: The aim of the present study is to verify whether Weizmannia coagulans BC 99 (BC99) can increase muscle mass and strength. Methods: This randomized double-blind, controlled trial assigned 72 male college students to receive probiotics (n = 36, 20.25 ± 1.03 years; 179.00 ± 5.94 cm; 73.55 ± 8.73 kg, protein powder with BC99) or the placebo (n = 36, 20.19 ± 0.79 years; 179.25 ± 5.16 cm; 73.61 ± 8.24 kg, protein powder) for 12 weeks. 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, and digestive enzymatic activity of stool samples, biochemical parameters, amino acids and hormone level of plasma were analyzed. Results: 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. Conclusions: Therefore, BC99 supplementation can be an important nutritional strategy to improve strength performance, body composition, protein digestion and body metabolism in healthy young males.