The present invention is directed to a processing method and a selection of ingredients that will retain TGF-β levels, bioactivity, and/or bioavailability in a liquid nutritional product. The method involves selecting one or more protein ingredients that have been subjected to a heat load comprising medium-heat or less; combining the protein ingredients with other components of the liquid nutritional product to form a slurry; subjecting the slurry to a pressure of from about 2500 psi to about 3500 psi at a temperature of from about 55° C. to about 65° C. for about 5 to 20 seconds; subjecting the slurry to a temperature of about 135 to 150° C. for about 1.5 to 15 seconds; and cooling the slurry to a temperature of less than about 8° C. over about 30 minutes or less.