Excessive body fat and obesity have adverse health effects and result in significant morbidity such as type 2 diabetes mellitus. The health burden of obesity can be reduced with the Roux-en-Y gastric bypass (RYGB) weight-loss bariatric surgery. Little is known on the molecular changes that occur at the metabolome level before and after bariatric surgery, with a view to clinical biomarker development. Hence, we employed a metabolomics approach in 10 obese diabetic patients who underwent bariatric surgery. Metabolomics data were obtained by T2- and diffusion-edited hydrogen nuclear magnetic resonance ((1)H NMR) spectra to monitor the metabolic and lipoprotein profiles, and gas chromatography-mass spectrometry (CG-MS) to access the fatty acid profile before and 12 months after RYGB. Using hierarchical partial least squares discriminant analysis, we found that RYGB induces several key metabolic alterations associated with glucose homeostasis, as well as fatty acid and amino acid metabolism. The levels of lactate (Krebs' intermediate cycle) decreased after RYGB. The leucine, isoleucine, valine, lactate, and glucose levels were higher in the samples before RYGB (p<0.05). Additionally, the levels of very low-density lipoprotein, unsaturated lipids, and N-acetyl-glycoprotein were higher before RYGB. By contrast, levels of the high-density lipoprotein and phosphatidylcholine were higher after bariatric surgery. These results collectively offer important holistic integrative biology data to develop future clinically relevant metabolomics biomarkers related to bariatric surgery in connection with obesity.