Background The potential impacts of beverage intake during the midlife on future subclinical atherosclerosis among women are unclear. The aim of this study was to evaluate the prospective associations between the intakes of eight beverage groups and subclinical carotid atherosclerosis in midlife women. Methods Data came from the Study of Women's Health Across the Nation, a multicenter, multiethnic, and prospective cohort study. A total of 1,235 midlife women had measures of subclinical carotid atherosclerosis and repeatedly beverage intake data collected using a validated food frequency questionnaire. Beverages were aggregated into eight groups, including coffee, tea, sugar-sweetened beverages, artificially sweetened beverages, fruit juices, whole milk, milk with lower fat content, and alcoholic beverages. The associations of beverage intake with common carotid artery intima-media thickness (CCA-IMT) and adventitial diameter (CCA-AD) were estimated using linear models; the associations with carotid plaque were estimated using log-binomial models. Results Coffee intake was associated with CCA-IMT in an inverted J-shaped pattern. After adjusting for covariates, women with >0 to <1 cup/day and 1 to <2 cups/day of coffee intake had a 0.031 mm (95% CI: 0.012, 0.051) and a 0.027 mm (95% CI: 0.005, 0.049) larger CCA-IMT, respectively, than coffee non-drinkers. Women who consumed ≥2 cups/day of coffee did not have significantly different CCA-IMT than non-drinkers. There was an inverse linear association between moderate alcoholic beverages intake and CCA-IMT (P-trend = 0.014). Whole milk intake had inverted U-shaped associations with CCA-IMT and carotid plaque. No significant associations were found between other beverage groups and subclinical atherosclerosis. Conclusions In midlife women, occasional coffee intake may be associated with more subclinical atherosclerosis while moderate alcoholic beverages intake may be associated with less subclinical atherosclerosis. Future work should focus on the determination of the optimal beverage intake profile for maximum cardiovascular benefits in midlife women.