Altered glucose metabolism via insulin resistance is a hallmark of type 2 diabetes (T2D), clinically observed as the inability to maintain postprandial blood glucose levels (BGL). Associated with energetic excess arising from caloric overload, T2D is linked to excess non-esterified fatty acid production and rising nutrient levels, which influence metabolic processes. The liver plays a pivotal role in the pathogenesis of T2D, via elevated gluconeogenesis, whereby glycogen stores are liberated, further elevating BGL. It is important to understand the molecular adaptations of the liver to the metabolic flux and insulin resistance arising from T2D. To achieve this we performed a multi-omic analysis including proteomics, lipidomics and metabolomics in a rat model of T2D combining the effects of high fat diet feeding (calorie overload) and streptozotocin (elevated BGL). To quantify alterations in protein abundance, samples were isobarically tagged prior to mass spectrometry (MS). Discovery lipidomics was achieved with relative quantitation by comparison with synthetic standards. Targeted metabolomics was performed using multiple reaction monitoring, in the presence of deuterated metabolite standards. We quantified close to 7,000 proteins, 300 lipid species and 100 metabolites in the course of this study. Proteomics revealed increased levels of proteins regulating phospholipid biosynthesis and fatty acid metabolism. A concurrent decrease in proteins involved in steroid biosynthesis was observed. Lipid analysis show increased sphingomyelin levels and decreased levels of phosphatidylcholines in T2D, both of which are components of cell membranes and can play a role in metabolic and apoptotic signalling. Elevated levels of branched chain amino acids as well as changes in metabolites indicative of altered energy and amino acid metabolism were detected by metabolomics. The current study has identified changes in protein, lipid composition and metabolite levels indicative of dysregulated energy utilisation and molecular adaptations that contribute to the pathogenesis of T2D.