Molecular biomarkers can complement dietary questionnaires through an objective quantification of food intake. The validation of biomarkers of food intake requests that the impact of extrinsic (e.g., food transformation) and intrinsic (e.g., human metabolism) factors be controlled. To investigate how milk fermentation and consumer age impact on markers of dairy intake, a randomized controlled crossover intervention study was conducted in 14 young and 14 older healthy men. Changes in the urinary metabolome after intake of milk and yogurt were measured after one single serving using three metabolomic platforms. The specificity of the urinary markers was further evaluated with a 19-d dietary restriction phase preceding the postprandial test during which the consumption of dairy products was eliminated and fermented foods were reduced. Profiling of the metabolome revealed a large number of features whose urinary relative abundance was modified by the milk fermentation status or participants’ age. Among these features 31 postprandially active metabolites could be identified (e.g., lactose and its metabolites or the aldehydes heptanal and nonanal). The validity of these candidate markers of dairy intake should be further investigated, in particular using multi-markers panels and under real life situation in observational cohorts.