Alteration of various metabolites has been linked to type 2 diabetes (T2D) and insulin resistance. However, identifying significant associations between metabolites and tissue-specific phenotypes requires a multi-omics approach. In a cohort of 42 subjects with different levels of glucose tolerance (normal, prediabetes and T2D) matched for age and body mass index, we calculated associations between parameters of whole-body positron emission tomography (PET)/magnetic resonance imaging (MRI) during hyperinsulinemic euglycemic clamp and non-targeted metabolomics profiling for subcutaneous adipose tissue (SAT) and plasma. Plasma metabolomics profiling revealed that hepatic fat content was positively associated with tyrosine, and negatively associated with lysoPC(P-16:0). Visceral adipose tissue (VAT) and SAT insulin sensitivity (K i), were positively associated with several lysophospholipids, while the opposite applied to branched-chain amino acids. The adipose tissue metabolomics revealed a positive association between non-esterified fatty acids and, VAT and liver K i. Bile acids and carnitines in adipose tissue were inversely associated with VAT K i. Furthermore, we detected several metabolites that were significantly higher in T2D than normal/prediabetes. In this study we present novel associations between several metabolites from SAt and plasma with the fat fraction, volume and insulin sensitivity of various tissues throughout the body, demonstrating the benefit of an integrative multi-omics approach. High-throughput metabolomics promises a deeper understanding of type 2 diabetes (T2D) mellitus 1. According to the World Health Organization's global report on diabetes, the age-standardized global prevalence of diabetes has nearly doubled from 1980 to 2014 2. Motivated by the necessity of progress to halt the diabetes epidemic, researchers have made significant discoveries to widen our understanding of T2D. A novel classification of T2D has been suggested, comprising of five clusters and reported to better correlate with disease progression and risk