The association between soy food and soy isoflavone intake and cardiovascular disease (CVD) risk is uncertain, especially in women. We aimed to investigate this association in Korean women. We analyzed data from the Korean Genome and Epidemiology Study, including 4713 Korean women aged 40–69 years with no CVD or cancer at baseline. Dietary information was obtained using a validated semi-quantitative food frequency questionnaire, and the incidence of CVD was assessed using biennial self-reported questionnaires on medical history. The mean follow-up time was 7.4 years, during which 82 premenopausal and 200 postmenopausal women reported CVD incidence. The highest tofu, total soy foods, and dietary soy isoflavone intake groups were significantly associated with a decreased CVD risk in premenopausal women (tofu: hazard ratio (HR) 0.39; 95% confidence interval (CI), 0.19–0.80; total soy food: HR 0.36; 95% CI, 0.18–0.70; dietary soy isoflavones: HR 0.44; 95% CI, 0.22–0.89), whereas no association was observed in postmenopausal women. Other soy foods showed no association with CVD incidence. Dietary soy isoflavones and total soy foods are associated with a decreased CVD risk in premenopausal women. Among soy foods, only tofu showed significant health benefits.