Milk processing may induce changes in dairy product composition and influence digestibility and nutrient bioavailability. Differences in protein degradation and peptide generation were studied for β-lactoglobulin and αS1-casein from commercially available dairy products before, during, and after in vitro digestion. All major milk proteins, except β-lactoglobulin, were degraded to smaller peptides during the gastric phase in all investigated products. After the gastric phase, a shortened fragment of β-lactoglobulin was identified in the non-fermented dairy products, underlining differences in protein conformation due to the fermentation process. During the gastric phase, greater numbers of small peptides were generated from αS1-casein than from β-lactoglobulin. The monitoring of generation of specific β-lactoglobulin and αS1-casein peptide profiles by liquid chromatography–mass spectrometry allowed the identification of potential bioactive peptides. Peptides with satiety-influencing DPP-4 inhibiting properties were monitored and quantities were compared between products to identify promising targets for the development of new health promoting products.