We assessed the relationship between a healthy lifestyle and the subsequent risk of developing metabolic syndrome. The “Seguimiento Universidad de Navarra” (SUN) Project is a prospective cohort study, focused on nutrition, lifestyle, and chronic diseases. Participants (n = 10,807, mean age 37 years, 67% women) initially free of metabolic syndrome were followed prospectively for a minimum of 6 years. To evaluate healthy lifestyle, nine habits were used to derive a Healthy Lifestyle Score (HLS): Never smoking, moderate to high physical activity (>20 MET-h/week), Mediterranean diet (≥4/8 adherence points), moderate alcohol consumption (women, 0.1–5.0 g/day; men, 0.1–10.0 g/day), low television exposure (<2 h/day), no binge drinking (≤5 alcoholic drinks at any time), taking a short afternoon nap (1 h/day, and working at least 40 h/week. Metabolic syndrome was defined according to the harmonizing definition. The association between the baseline HLS and metabolic syndrome at follow-up was assessed with multivariable-adjusted logistic regressions. During follow-up, we observed 458 (4.24%) new cases of metabolic syndrome. Participants in the highest category of HLS adherence (7–9 points) enjoyed a significantly reduced risk of developing metabolic syndrome compared to those in the lowest category (0–3 points) (adjusted odds ratio (OR) = 0.66, 95% confidence interval (CI) = 0.47–0.93). Higher adherence to the Healthy Lifestyle Score was associated with a lower risk of developing metabolic syndrome. The HLS may be a simple metabolic health promotion tool.