To investigate the longitudinal association of different phenotypes of diabetes and obesity with the incidence of cardiovascular disease (CVD), CVD- and all-cause mortality. A total of 5432 adults, aged ≥ 35 years and free of CVD were included in this cohort study. Diabesity phenotypes were defined in six categories based on the presence of diabetes (normal (NG), prediabetes and diabetes) and obesity (obese, non-obese). Fasting blood sugar, 2-h post prandial glucose, or using anti-diabetic medicines were used to define diabetes, and body mass index and waist circumference were used to define obesity. Cox proportional hazards models were used to estimate hazard ratios (HRs) for incident CVD, CVD- and all-cause mortality across these categories. After a median follow-up of 11.25 years, 819 CVD cases, 181 CVD deaths and 488 all-cause deaths occurred. In multivariable-adjusted models and irrespective of obesity definition, the phenotypes of normal glucose-obese, prediabetes-obese and pre-diabetes-non obese were not associated with CVD incidence in comparison with NG-non obese phenotype, however, the phenotypes of diabesity, either defined by general or abdominal obesity, were associated with increased risk of incident CVD events (HR = 1.42, 95% CI 1.01, 1.99, and HR = 1.46, 95% CI 1.07, 1.98, respectively). These findings were sex-specific and only in men with a phenotype of abdominal obesity-diabetes, a positive link was observed for CVD incidence (HR = 1.60, 95% CI 1.01, 2.52). No significant association was found between diabesity and death from CVD or all causes. Diabesity is a predictor of CVD and stroke incidence, but not CVD or all-cause mortality, among Iranians. This association is more pronounced amongst men than women.