Previous studies found variations in the health-promoting effects of consuming different dairy products. This study aims at investigating the chemical composition of microbial fermented yogurt, chemically acidified yogurt and whole milk to understand the differences in the effects these products exert on human health. For this purpose, peptides and small compounds present in the products were examined using a combination of liquid chromatography mass spectrometry and nuclear magnetic resonance spectroscopic techniques. Results revealed that each product had its own characteristic peptide, free amino acid and small compound profile, and database search for bioactivity disclosed that fermented yogurt manufactured using a starter culture is associated with a higher bioactivity potential than chemically acidified yogurt or whole milk. Additional cold storage (14 days) further enhances the bioactivity potential of fermented yogurt while heat-inactivation, ensuring long shelf-life, modulates the proteins available for proteolysis and thereby the peptide profile generated.