AimTo assess the effect of obesity phenotype on the incidence of diabetes, considering phenotype as a time‐varying exposure.MethodsWe used community‐based cohort data from the Korean Genome and Epidemiology Study, with a 16‐year follow‐up period. Obesity phenotype was determined using body mass index and metabolic syndrome criteria. The influence of obesity phenotype on the occurrence of diabetes was evaluated using a Cox proportional hazard model and a marginal structural model (MSM).ResultsObesity phenotypes were defined in 6265 individuals, with diabetes identified in 903 (14.4%) during the follow‐up period. Individuals with metabolically healthy obesity (MHO) exhibited a higher risk of diabetes compared to those with metabolically healthy normal weight (MHNW), with a hazard ratio (HR) of 1.48 (95% confidence interval [CI] 1.15‐1.90). This association remained significant after applying the MSM (HR 1.49, 95% CI 1.01‐2.20). Moreover, various sensitivity analyses consistently demonstrated a higher risk of diabetes in individuals with MHO compared to those with MHNW.ConclusionsEven when obesity phenotype was treated as a time‐varying exposure, individuals with MHO were still at higher risk for developing diabetes than those with MHNW. Consequently, such individuals should aim to avoid transitioning to a metabolically unfavourable state and strive to reduce their body weight to a normal range.