In the present study, it was evaluated whether microencapsulated cocoa supplementation could attenuate endothelial dysfunction caused by eccentric exercise in healthy subjects. Thirteen volunteers were enrolled in this double-blind, placebo-controlled, crossover study. Flow-mediated dilatation (FMD), blood flow and muscle O2 saturation (StO2) were evaluated by ultrasound and near-infrared spectroscopy (NIRS), respectively, before and after microencapsulated cocoa supplementation. The eccentric exercise was performed after microencapsulated cocoa supplementation to generate vascular dysfunction. Eccentric exercise significantly reduced FMD in the PLA condition, but cocoa attenuated this exercise effect. No significant effect was observed on muscle StO2 and blood flow after eccentric exercise and nutritional supplementation. In conclusion, the present study showed that a single dose of microencapsulated cocoa ingestion attenuated FMD-induced eccentric exercise. These findings suggest that a single dose of microencapsulated cocoa may be an alternative nutritional strategy to attenuate vascular dysfunction induced by eccentric exercise in healthy individuals.