Dairy proteins are an important part of our diet, and recently, there is considerable focus on understanding the effects of the two major dairy proteins fractions constituted by casein and whey. In the present study, the impact of a dietary intervention with casein, whey, and skim milk was investigated by using NMR-based urine metabolomics. Overweight adolescents (n = 192; age = 12–15 years; BMI = 25.4 ± 2.3 kg/m²) were randomly assigned to 1 L/day of casein (citrate content: 3.27 mol/L), whey (citrate content: 0.04 mol/L), skim milk, or water for 12 weeks. A significant increase in the urinary excretion of urea was found after the 12-week casein and skim milk interventions, while the 12-week whey intervention had no significant effect on the urea excretion. In addition, NMR-based metabolomics revealed a decreased urinary citrate excretion in the whey group and thereby demonstrated its potential to disclosure exposure effects. In conclusion, the present study demonstrates that casein and whey proteins impact urinary urea excretion differently.