Background/Objectives: Metabolic syndrome (MetS) is a heterogeneous cluster of car-diometabolic risk factors whose underlying molecular heterogeneity remains incompletelyunderstood. Methods: Targeted metabolomics (388 metabolites) and untargeted pro-teomics (842 proteins) were analyzed in the KORA FF4 study (n = 1921). Multivariableregression, LASSO, and Multi-Omics Factor Analysis (MOFA) were applied to identify MetS-associated signatures. As a secondary analysis, soft-clustering archetypal analysis based on22 clinical variables was performed within the MetS subgroup (n = 582) to identify extremeclinical subphenotypes. Results: A total of 117 metabolites and 70 proteins were associatedwith MetS, including five metabolites and eight proteins shared across all MetS traits. Keymetabolomic features comprised diacylglycerols, triglyceride score, hexoses, and branched-chain amino acids. Prominent proteins included APOC4, APOE, APOB, APOD, APOF,adiponectin, LBP, and SHBG, reflecting alterations in lipid metabolism, inflammation, andmetabolic regulation. MOFA identified a latent factor strongly linked to MetS, integratingsignatures of lipid metabolism, insulin resistance, and inflammation. Archetypal analysisidentified extreme MetS profiles and associated with metabolites and proteins shared acrossall Mets. Conclusions: Integrated multi-omics analysis revealed MetS-associated molecularsignatures characterized primarily by dysregulated lipid metabolism, insulin resistance,and chronic low-grade inflammation. Secondary archetypal analysis highlighted clinicalheterogeneity at the extreme boundaries of MetS while supporting a shared molecularfoundation. These findings highlight the value of combining clinical, metabolomics andproteomics to improve characterization of MetS heterogeneity and inform future precisionrisk stratification.