Impaired intestinal permeability can induce systemic inflammation and metabolic disturbance. However, the effect of impaired intestinal permeability on metabolic function in the skeletal muscle is unknown. Dietary polysorbate 80 (PS80), a common emulsifier, has been shown to impair intestinal permeability in mice. Here, we investigated the effect of PS80‐induced intestinal permeability on glucose tolerance with metabolic signaling in the skeletal muscle. Male ICR mice were divided into control and PS80 groups. In the PS80 group, PS80 was contained in the drinking water at 1% (w/v). After 4 weeks, plasma fluorescein isothiocyanate (FITC) intensity was measured after orally administering FITC‐dextran. Half of the mice in each group underwent running exercises. Metabolic and inflammatory parameters were examined in the blood and skeletal muscle. Plasma FITC and lipopolysaccharide levels were higher in the PS80 group than the control group (p < .01, p = .085). The expression of tumor necrosis factor‐α in the skeletal muscle was increased upon PS80 administration (p < .05). Although the homeostasis model assessment ratio was higher in the PS80‐fed mice (p < .05), insulin‐signaling activity in the muscle did not differ between groups. Muscular pH, mitochondrial cytochrome oxidase activity, and glycogen content after exercise were lower in the PS80 group (p < .05) than the control group. There was a negative correlation between plasma FITC and muscle glycogen levels in the exercised groups (r = −.60, p < .05). These results suggest that daily PS80 intake induces intestinal permeability, leading to glucose intolerance and mitochondrial dysfunction in the skeletal muscle.