Purpose This prospective population-based study investigated whether having any internalizing mental disorder (INT) was associated with the presence and onset of any cardiometabolic disorder (CM) at 3-year follow-up; and vice versa. Furthermore, we examined whether observed associations differed when using longer time intervals of respectively 6 and 9 years. Methods Data were used from the four waves (baseline and 3-, 6- and 9-year follow-up) of the Netherlands Mental Health Survey and Incidence Study-2, a prospective study of a representative cohort of adults. At each wave, the presence and first onset of INT (i.e. any mood or anxiety disorder) were assessed with the Composite International Diagnostic Interview 3.0; the presence and onset of CM (i.e. hypertension, diabetes, heart disease, and stroke) were based on self-report. Multilevel logistic autoregressive models were controlled for previous-wave INT and CM, respectively, and sociodemographic, clinical, and lifestyle covariates. Results Having any INT predicted both the presence (OR 1.28, p = 0.029) and the onset (OR 1.46, p = 0.003) of any CM at the next wave (3-year intervals). Having any CM was not significantly related to the presence of any INT at 3-year follow-up, while its association with the first onset of any INT reached borderline significance (OR 1.64, p = 0.06), but only when examining 6-year intervals. Conclusions Our findings indicate that INTs increase the risk of both the presence and the onset of CMs in the short term, while CMs may increase the likelihood of the first onset of INTs in the longer term. Further research is needed to better understand the mechanisms underlying the observed associations.