Heat treatment is a widely used method for food processing, and the compounds formed by heat processes may serve as biomarkers of heated food intake in nutrition studies. Therefore, we aimed to characterize the differential metabolic signatures resulting from intake of different potato products and identify potential intake biomarkers. In a randomized, controlled, crossover meal study, healthy volunteers consumed boiled rice, boiled potatoes, and two deep-fried potato products, potato chips and French fries. The urine metabolome was acquired by LC-MS-based untargeted metabolomics. Twenty-two selected metabolites were found for deep-fried potatoes, two for potato intake in general, and one for boiled rice. Fourteen of the 22 selected metabolites were tentatively identified as furan-, pyrrole- and pyrazine-derived compounds indicative of Maillard reactions. With further validation, these candidate biomarkers will be important tools to investigate the influence of heated foods on human health.