Metabolic syndrome (MetS) is a widespread and complex health disorder. Dietary habits and consumption of simple sugars have been shown to play an important role in the prevention and treatment of MetS. This cross-sectional study was conducted in a population of 3380 adults from the Shiraz University of Medical Sciences (SUMS) employees’ health cohort. The healthy beverage index (HBI) and healthy beverage score (HBS) were calculated. Risk for MetS and its components, including blood pressure, fasting blood glucose, waist circumference, triglyceride levels, and high-density lipoprotein cholesterol, were measured using standardised protocols. Results showed a significant inverse association between higher adherence to HBI (OR = 0.60, 95% CI: 0.48–0.74, P < 0.001) and HBS (OR = 0.80, 95% CI: 0.65–0.97, P = 0.030) with lower risk of MetS. Also, we observed a significant association between higher level of HBI and HBS with decreased risk of hypertension, as a critical component of MetS. These findings support the notion that healthier beverage consumption, as indicated by higher HBI and HBS levels, may play a critical role in reducing the risk of MetS.