Lower socio-economic status (SES) is significantly associated with metabolic syndrome (MS) prevalence, possibly affecting women more than men, although evidence in Spain is still limited. The present cross-sectional study analyzed the association between MS and SES by age and gender among 42,146 working adults living in the Balearic Islands (Spain). Prevalence was higher in men (9.4% by ATP-III; 12.3% by IDF) than women (3.8% by ATP-III; 5.7% by IDF) and in the lower social class (7.9% by ATP-III; 10.7% by IDF) than the higher (4.1% by ATP-III; 5.9% by IDF). The SES gradient in MS prevalence was larger in women (PR 95% CI: 3.38, 2.50–4.58 by ATP-III; 3.06, 2.43–3.86 by IDF) than in men (1.23, 1.06–1.41 by ATP-III; 1.15, 1.03–1.30 by IDF) and was already evident from early adulthood, reaching the highest ratio at the late stages of middle adulthood (4.34, 1.11–16.98). Among men, it was significant during the late stages of early adulthood only (1.80, 1.19–2.73). Lower SES influenced MS prevalence in both genders, however, women seemed more affected than men. From a public health perspective, SES could be strongly associated with the burden of MS; in an effort to reduce its prevalence, public health policies should focus on gender differences in socio-economic inequality and consider women with low socio-economic resources as a priority.