MPCs/MPIs have a clean, light, milky flavor compared to WPCs/WPIs. As WPC/WPIs are a byproduct of cheese production, they can have various off-flavors due to processing such as sourness, bitterness, and broth-like. These off-flavors result from high usage levels of sodium, potassium, and chlorine. Whey proteins may also bind volatile flavor compounds during processing. In cheese making, the flavor of WPC can greatly depend on the type of cheese it was made from and the processing facility. The main sources of off flavors in WPC are from volatile lipid oxidation compounds which occur in the cheese making process. Protein degradation also occurs in this process, which leads to undesirable flavors and can have nutrition implications.

Astringency can also be a problem when protein levels are too high. Astringency is a dry, puckery mouth-feel. Although this can be a problem in both MPC/MPI and WPC/WPI, studies have shown that the mouth drying effect of astringency was significantly higher with WPC beverages compared to MPC beverages.