Metabolic syndrome (MetS) is a disorder characterized by a group of factors that can increase the risk of chronic diseases, including cardiovascular diseases and type 2 diabetes mellitus (T2D). Metabolomics, the study of small molecules on a large scale, commonly called metabolites, within cells, biofluids, tissues, or whole organisms, has provided new insight into disease diagnosis and biomarkers identification. In the current study, a cross-sectional investigation was conducted using an untargeted metabolomics-based technique to identify metabolomic alterations and their relationship to pathways in normoglycemic and prediabetic MetS participants to improve disease diagnosis. Moreover, targeted analysis was done for two metabolites: carnitine and choline. Plasma samples were collected from drug-naïve prediabetic MetS patients (n=26), normoglycemic MetS patients (n=30), and healthy (normoglycemic lean) subjects (n=30) who met the inclusion criteria for the study. The plasma samples were analyzed using a highly sensitive ultra-high performance liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). One-way ANOVA analysis revealed that 59 metabolites differ significantly among the three groups (p <0.05). Glutamine, 5-hydroxy-L-tryptophan, L-sorbose, and hippurate were highly associated with normoglycemic MetS. However, 9-methyluric acid, sphinganine, and threonic acid were highly associated with prediabetes MetS. Metabolic pathway analysis showed that arginine biosynthesis and glutathione metabolism were associated with MetS/prediabetes, while phenylalanine metabolism, D-glutamine and D-glutamate metabolism, and lysine degradation were highly impacted in MetS. The current study sheds light on the potential diagnostic value of some metabolites in metabolic syndrome and the role of their alteration in some metabolic pathways. More studies are needed in larger cohorts in order to verify the implication of the above metabolites on MetS and