Introduction Improved knowledge of prediabetic subjects’ profile and their risk of developing type 2 diabetes mellitus (T2DM) would enhance secondary prevention. The primary objective is to describe factors associated with incident T2DM in subjects with pre-diabetes diagnosed in primary care. Methods and analysis The study is based on Reunion Island, a French overseas region that experiences a particularly high disease burden of T2DM. This is an observational, non-randomised prospective cohort study conducted in primary care in which private general practitioner (GP) investigators recruit participants with pre-diabetes from their practices regardless of the initial motive for consultation. Pre-diabetes is defined by WHO criteria, that is, fasting plasma glucose between 1.10 g/L and 1.25 g/L and/or plasma glucose 2 hours after ingestion of 75 g of glucose (2-hour post load plasma glucose) between 1.40 g/L and 1.99 g/L. The design is based on an annual follow-up by the GP (according to French National Health Authority recommendations) with collection of clinical and laboratory data and specific lifestyle questionnaires answered by telephone at three time points: inclusion, and at 2-year and 5-year follow-up visits. Follow-up clinical and laboratory data are collected by the investigating GP as part of the study, and study-specific laboratory collections (serum, DNA and urine) will be obtained 2 and 5 years after inclusion. The primary outcome is transition to T2DM. Ethics and dissemination This protocol has been approved by the research ethics committee of Saint Etienne (CPP Saint Etienne reference number: 2019–03). Enrolment began in August 2019. Results will be disseminated in at least three papers published in peer-reviewed medical journals, one oral communication and a large-scale communication to the local population and healthcare policymakers. Trial registration number NCT04463160 and ID-RCB 2018-A03106-49.