The association between the metabolic syndrome (MetS) and adverse outcomes in older adults may be explained by other health conditions. This study examined the role of frailty in explaining the association between MetS and mortality, independent of comorbidity. Data were used from 1247 men and women aged ≥ 65 years of the Longitudinal Aging Study Amsterdam. MetS was assessed using the definition of the US National Cholesterol Education Program. Frailty was measured by the frailty phenotype. Mortality was monitored from 1995 until 2015. Associations of MetS with 19-year all-cause mortality were assessed using Cox proportional hazard models. MetS was present in 37% of the participants. In a model adjusted for age, sex and educational level hazard ratios of mortality were significantly higher in people with MetS (HR = 1.23, 95% CI = 1.08–1.40). After adjusting for frailty the association of MetS with mortality reduced, but remained statistically significant (HR = 1.15, 95% CI = 1.01–1.31). The presence of chronic diseases (cardiovascular diseases and diabetes) explained a larger part of the relationship between MetS and mortality (HR = 1.12, 95% CI = 0.98–1.28). These results show that physical frailty has a smaller contribution to the explanation of the association between MetS and 19-year all-cause mortality than the presence of chronic diseases.