Health parameters, performance and body composition effects produced by twelve weeks of intervention with hydrolysed whey protein in elite soccer players from a Brazilian team during an actual championship were compared. Twenty-four players were divided into three groups according to supplement: whey protein (WP), hydrolysed whey protein (HWP), or a non-protein placebo (maltodextrin, MALTO). Biochemical, anthropometric and performance tests were applied on week 0 and week 12 of the intervention. Intervention with hydrolysed whey protein resulted in significant decreases in the muscle damage indicators, creatine kinase (−42%) and lactate dehydrogenase (−30%), compared with increases in the MALTO group. Supplementation with whey protein showed no significant changes in these indicators compared with the MALTO group. Muscle mass showed no changes, and physical performance in an aerobic test was decreased in the HWP group compared with the MALTO and WP groups. These data suggest that the consumption of HWP decreases muscle damage.