We aim to determine the association between Fe status and the metabolic syndrome (MetS) during menopause. Records of 1069 premenopausal and 703 postmenopausal Korean women were retrieved from the database of the fifth Korean National Health and Nutrition Examination Survey (KNHANES V 2012) and analysed. The association between the MetS and Fe status was performed using multivariable-adjusted analyses, subsequently develop a prediction model for the MetS by margin effects. We found that the risk of Fe depletion among postmenopausal women was lower than premenopausal women (PR = 0·813, 95 % CI 0·668, 0·998, P = 0·038). The risk of the MetS was 2·562-fold lower among premenopausal women with than without Fe depletion (PR = 0·390, 95 % CI 0·266, 0·571, P < 0·001). In contrast, the risk of the MetS tended to be higher among postmenopausal women with than without Fe depletion (PR = 1·849, 95 % CI 1·406, 2·432, P < 0·001). When the serum ferritin levels increased, the risk of the MetS increased in both premenopausal women and postmenopausal women. The margin effects showed that an increase in serum Hb and ferritin was associated with an increase in the risk of the MetS according to menopausal status and age group. Therefore, ferritin is the most validated and widely used Fe marker, could be a potential clinical value in predicting and monitoring the MetS during menopause. Further prospective or longitudinal studies, especially, clinically related studies on menopause and Fe status, are needed to clarify the causality between serum ferritin levels and the MetS that could offer novel treatments for the MetS.