Characterization of metabolic changes is key to early detection, treatment, and understanding molecular mechanisms of diabetes. Diabetes represents one of the most important global health problems. Approximately 90% of diabetics have type 2 diabetes. Identification of effective screening markers is critical for early treatment and intervention that can delay and/or prevent complications associated with this chronic disease. Fortunately, metabolomics has introduced new insights into the pathology of diabetes as well as to predict disease onset and revealed new biomarkers to improve diagnostics in a range of diseases. Small-molecule metabolites have an important role in biological systems and represent attractive candidates to understand T2D phenotypes. Characteristic patterns of metabolites can be revealed that broaden our understanding of T2D disorder. This technique-driven review aims to demystify the mechanisms of T2D, to provide updates on the applications of metabolomics in addressing T2D with a focus on metabolites based biomarker discovery.