Aims: To determine the association between serum levels of vitamin B12 and metabolic syndrome (MetS) in a population of euthyroid adults. Materials and methods: We carried out an analytical cross-sectional study in euthyroid adults of both sexes, who attended the outpatient service of a private clinic in Lima-Peru during the 2012–2016 period. Participants were divided into tertiles (low, intermediate and high) according to their serum vitamin B12 values. MetS was defined when three or more metabolic criteria were met by the participants. We elaborated crude and adjusted Poisson regression models to evaluate the association between the serum vitamin B12 tertiles and the presence of MetS. The reported association measure was the prevalence ratio (PR) with their respective 95% confidence intervals (95%CI). Results: We analyzed 346 participants, the average age was 38.3 ± 10.8 (SD) years, 117 (33.8%) were males, the serum vitamin B12 median was 364.1 (IQR: 274.2–473.4) pmol/L and the prevalence of MetS was 30.1% (n = 104). In the crude Poisson regression model, we found an association between the serum vitamin B12 tertiles and the presence of MetS, with marginal significance. The association gained statistical significance in the adjusted model by potential confounders; and compared with the low serum vitamin B12 tertile, the prevalence of MetS was 36% lower (aPR = 0.64; 95%CI: 0.43–0.96) among the high tertile group. Conclusion: Euthyroid participants with elevated levels of serum vitamin B12 showed a lower prevalence of MetS compared to those who had low levels of this marker.