Purpose We examined the effect on the postprandial plasma metabolome of protein pre-meals before a fat-rich main meal. Methods Two randomized, cross-over meal studies were conducted to test the dose-response effect (0 g, 10 g, 20 g) of a pre-meal with whey protein (WP) (PREMEAL I), and the effect of protein quality (10 g WP, casein, or gluten) and timing (- 15 min vs - 30 min) of the pre-meal (PREMEAL II). Participants with metabolic syndrome received one of the test meals on each test day, - 15 min (or - 30 min) prior to a standardized fat-rich breakfast. Plasma samples were collected at - 15 min (or - 30 min), 0, 120, 240 a nd 360 min and analyzed using liquid chromatography-mass spectrometry with an untargeted method. Results Pre-meal WP intake elevated plasma branched-chain amino acids (BCAA), aromatic amino acids and methionine and decreased plasma LPC (16:0) and PC (32:1) levels before the main meal. Early (- 15 to 0 min) aromatic amino acids and BCAA in response to pre-meal WP partially predict the glucose and insulin response after the main meal. A pre-meal with WP altered the postprandial plasma metabolic pattern of acyl-carnitines, specific PCs, LPCs and LPEs, betaine, citric acid, linoleic acid, and beta-hydroxypalmitic acid compared to no pre-meal. The casein and WP pre-meals exhibited similar postprandial amino acid responses whereas a pre-meal with gluten resulted in lower levels of plasma amino acids and its metabolites. Conclusion A pre-meal with protein affects the postprandial metabolic pattern indicating facilitated glucose and lipid disposal from plasma in participants with metabolic syndrome.