Abstract: The invention relates to processes for manufacturing stable functional protein-containing beverage compositions, such as dairy-based beverages. A functional ingredient, such as yeast beta-glucan, is stabilized in the protein-containing composition by subjecting the composition to intense agitation, e.g. homogenization or sonication. Advantageously, these processes permits heat-treatment of the functional beverage composition for extended shelf-life of the final product. Stable functional beverage compositions prepared by these processes are also provided.