Abstract Background Individuals with frailty are at increased risk of type 2 diabetes (T2D), but the underlying mechanisms are unclear. We aimed to investigate whether the frailty-T2D association is mediated by alterations in the metabolome and assess potential interaction with genetic susceptibility to diabetes. Methods This retrospective analysis, using data from a large prospective population-based cohort, included a total of 197,502 adults with baseline metabolomics data from the UK Biobank. Frailty was defined using the Fried frailty phenotype according to five components. Elastic net regression was applied to create a frailty-related metabolic signature. We assessed hazard ratios (HR) and its 95% confidence interval (CI) of incident T2D in relation to the baseline metabolic signature of frailty and examined the mediating role of the metabolic signature in the effect of frailty on T2D. Additive interaction between the metabolic signature and polygenic risk score for T2D (PRS-T2D) on the incidence of T2D was assessed as relative excess risk due to interaction (RERI). Results Compared with non-frailty, the HR (95% CI) of incident T2D in pre-frailty and frailty was 1.33 (1.26, 1.40) and 1.59 (1.46, 1.74), respectively. The metabolic signature of frailty (comprised of 53 metabolites) was positively associated with T2D risk (HR per standard deviation increment: 1.45; 95% CI: 1.42, 1.48), and explained 31.0% (95% CI: 25.8, 36.8) of the association between frailty and T2D. An additive interaction between metabolic signature of frailty and PRS-T2D was found (RERI: 9.43; 95% CI: 6.06, 12.80). Conclusions The increased risk of T2D in individuals with frailty may be mediated through effects on the metabolome, and the influence of such metabolic alterations on diabetes risk may be amplified in individuals with genetic susceptibility to T2D. Graphical abstract