The prevalence of prediabetes is increasing world-wide. Prediabetes is not only associated with an increased risk of type 2 diabetes and cardiovascular disease (CVD), but also of dementia and cancer, and, therefore, has recently gained much attention in the field of clinical research. In prediabetes lifestyle and pharmacological intervention can prevent diabetes and possibly CVD. Thus, the implementation of interventions in this condition is of major importance. However, prediabetes is a very heterogeneous metabolic state, both in respect to its pathogenesis and prediction of diseases. Thus, better understanding of its pathophysiology and stratification of the risk should be done. This can be achieved by applying precise phenotyping strategies. It will be discussed how stratification of individuals with prediabetes at baseline into a high-risk and a low-risk phenotype, based on corrected insulin secretion and insulin-resistant NAFLD, may help to determine the effectiveness of a lifestyle intervention to revert individuals to normal glucose regulation. By addressing evidence that has derived from lifestyle intervention studies the further aim ist to clarify whether these phenotypes can be used for individualized prediction and prevention of cardiometabolic diseases in prediabetes.