Type 2 diabetes is routinely identified in clinical practice by tests that rely on a hyperglycemic index. However, people at risk for developing type 2 diabetes may not present with hyperglycemia. We identified several underlying risks for type 2 diabetes, insulin resistance, and associated co-morbidities, using a liquid chromatography mass spectrometry–based analysis of blood metabolites, in participants with normoglycemia and no clinical symptoms. Personalized lifestyle recommendations, including diet, exercise, and nutritional supplement recommendations, were conveyed to these participants by a web-based platform, and after 100 days of following their recommendations, these participants reported reductions in the health risks associated with type 2 diabetes and associated diseases. Our comprehensive metabolite-based assay can be used for type 2 diabetes risk stratification, and our personalized lifestyle recommendation system could be deployed as a preventative treatment option to improve health outcomes, reduce the incidence of chronic disease, and live healthier lives in an evidence-based way.