(1) Background: Metabolic Syndrome (MetS) affects over a third of the United States population, and has similar prevalence in Europe. Dietary approaches to prevention are important. Coffee consumption has been inversely associated with mortality and chronic disease; however, its relation to the risk of MetS is unclear. We aimed to investigate the association between coffee consumption and incident MetS in the ‘Seguimiento Universidad de Navarra’ cohort. (2) Methods: From the SUN project, we included 10,253 participants initially free of MetS. Coffee consumption was assessed at baseline, and the development of MetS was assessed after 6 years of follow-up. All data were self-reported by participants. MetS was defined according to the Harmonizing Definition. We used multivariable logistic regression models to estimate odds ratios and 95% confidence intervals for incident MetS according to four categories of coffee consumption: <1 cup/month; ≥1 cup/month to <1 cup/day; ≥1 cup/day to <4 cups/day; ≥4 cups/day. (3) Results: 398 participants developed MetS. Coffee consumption of ≥1 to <4 cups/day was associated with significantly lower odds of developing MetS (multivariable adjusted OR = 0.71, 95% CI (0.50–0.99)) as compared to consumption of <1 cup/month. (4) Conclusions: In a Mediterranean cohort, moderate coffee consumption may be associated with a lower risk of MetS.