A challenge of shelf stable beverages that contain whey protein is that a small portion of protein can be denatured and aggregated during thermal processing, resulting in a turbid solution or white precipitate that consumers perceive as a defect. In this study, 3 approaches were taken to reduce turbidity in heat-treated beverages that contain whey protein: (1) centrifugation to remove insoluble protein aggregates, (2) addition of ingredients, and (3) alteration of pH in the range from 3.0 to 4.0. At pH 3.6 and below, all samples were essentially clear both before and after heating for all ingredients. At a pH of 3.8 and above, ingredient selection was crucial to solution clarity after heat treatment. At a pH of 4.0, addition of salts at both 10 and 50 mM increased the turbidity significantly compared to the control, which contained only whey protein in water. Neither addition of sugars at 25, 50, and 100 g/L, nor addition of sugar alcohols at 25 g/L significantly affected turbidity after heat treatment compared to the control. However, sugar alcohols added at 50 or 100 g/L significantly reduced turbidity after heat treatment compared to the control. Removal of insoluble protein aggregates by centrifugation prior to heat treatment resulted in a statistically significant decrease in turbidity after heat treatment. Understanding these results at the molecular level will assist food scientists in selecting processing treatments, ingredients, and pH in the development of shelf stable clear beverages that contain whey protein.