Although supplementation with several antioxidants has been suggested to improve aerobic metabolism during exercise, whether dietary foods containing such antioxidants can exert the metabolic modulation is unclear. This study aimed to investigate the effect of intake of the specific antioxidant-rich foods coupled with exercise training on energy metabolism. Twenty young healthy, untrained men were assigned to antioxidant and control groups: participants in the antioxidant group were encouraged to consume foods containing catechin, astaxanthin, quercetin, glutathione, and anthocyanin. All participants performed cycle training at 60% maximum oxygen consumption for 30 min, 3 days per week for 4 weeks. Maximum work load was significantly increased by training in both groups, while oxygen consumption during exercise was significantly increased in the antioxidant group only. There were positive correlations between maximum work load and fat/carbohydrate oxidations in the antioxidant group. Carbohydrate oxidation during rest was significantly higher in the post-training than that in the pre-training only in the antioxidant group. More decreased levels of serum insulin and HOMA-IR after training were observed in the antioxidant group than in the control group. This study suggests that specific antioxidant-rich foods could modulate training-induced aerobic metabolism of carbohydrate and fat during rest and exercise.