Metabolomics has been utilized in epidemiological studies to investigate biomarkers of nutritional status and metabolism in relation to non-communicable diseases. However, little is known about the effect of prandial status on several biomarker concentrations. Therefore, the aim of this intervention study was to investigate the effect of a standardized breakfast meal followed by food abstinence for 24 h on serum concentrations of amino acids, one-carbon metabolites, and B-vitamin biomarkers. 34 healthy subjects (18 males and 16 females) aged 20-30 years were served a breakfast meal (∼500 kcal) after which they consumed only water for 24 hours. Blood samples were drawn before, and at 13 standardized timepoints after the meal. Circulating concentrations of most amino acids and metabolites linked to one-carbon metabolism peaked within the first three hours after the meal. The branched-chain amino acids steadily increased from six or eight hours after the meal, while proline decreased in the same period. Homocysteine and cysteine concentrations immediately decreased after the meal but steadily increased from three and four hours until 24 hours. Flavin mononucleotide and riboflavin fluctuated immediately after the meal but increased from 6 hours, while folate increased immediately after the meal and remained elevated during the 24 hours. Our findings indicate that accurate reporting of time since last meal is crucial when investigating concentrations of certain amino acids and one-carbon metabolites. Our results suggest a need for caution when interpretating studies which utilize such biomarkers, but do not strictly control for time since the last meal.