ScopeTo identify metabolites associated with habitual dairy consumption and investigate their associations with type 2 diabetes (T2D) risk.Methods and resultsMetabolomics assays were conducted in the Fenland (n = 10,281) and EPIC‐Norfolk (n = 1,440) studies. Using 82 metabolites assessed in both studies, we developed metabolite scores to classify self‐reported consumption of milk, yogurt, cheese, butter, and total dairy (Fenland Study‐discovery set; n = 6035). Internal and external validity of the scores was evaluated (Fenland‐validation set, n = 4246; EPIC‐Norfolk, n = 1440). The study assessed associations between each metabolite score and T2D incidence in EPIC‐Norfolk (n = 641 cases; 16,350 person‐years). The scores classified low and high consumers for all dairy types with internal validity, and milk, butter, and total dairy with external validity. The scores were further associated with lower incident T2D: hazard ratios (95% confidence interval) per standard deviation: milk 0.71 (0.65, 0.77); butter 0.62 (0.57, 0.68); total dairy 0.66 (0.60, 0.72). These associations persisted after adjustment for known dairy‐fat biomarkers.ConclusionMetabolite scores identified habitual consumers of milk, butter, and total dairy products, and were associated with lower T2D risk. These findings hold promise for identifying objective indicators of the physiological response to dairy consumption.