Scope: Understanding the mode-of-action by which fermented dairy consumption influences health is of interest. The aim of this study is to elucidate the impact of the chemical-physical properties of the dairy matrix and postbiotic effects on the metabolomics response to fermented dairy consumption. Methods and results: Hundred males (Body Mass Index (BMI) 28.0–45.0 kg m⁻², waist circumference ≥ 102 cm) are included in the study. During a 16-week intervention, the study subjects are instructed to consume 400 g per day of either 1) milk, 2) yogurt, 3) heat-treated yogurt, or 4) chemically acidified milk as part of their habitual diet. Nuclear Magnetic Resonance (NMR)-based metabolomics is conducted on plasma, urine, and fecal samples collected before and after the intervention. Both consumption of acidified milk and heat-treated yogurt resulted in changes in the fecal metabolome including decreases in the level of amino acids (leucine, valine, and threonine), and the branched-chain fatty acid (BCFA) isobutyrate that indicated an altered protein putrefaction, and proteolytic metabolism in the gut. In the plasma metabolome, an increased citrate is found for yogurt consumption. No difference in the urine metabolome is found. Conclusions: Our metabolomics analyses indicate that consumption of heat-treated yogurt and acidified milk exerted similar effects on the metabolic activity in the gut as yogurt consumption.