Disclosed are substantially clear nutritional liquids comprising protein and calcium HMB wherein soluble protein represents from about 65% to 100% by weight of total protein. The liquids have a pH of from about 2.8 to about 4.6 and may be manufactured as a hot fill product. The substantially clear nutritional liquids may also have a weight ratio of calcium HMB to soluble calcium of from 4.5:1 to 7.3:1. In some embodiments, the substantially clear nutritional liquids are substantially free of fat, and may optionally include isomaltulose and/or beta alanine.