The exercise-induced muscle damage is associated with symptoms such as inflammation, delayed onset muscle soreness and impaired muscle performance. Cocoa polyphenols intake has been suggested to improve muscle recovery due to their antioxidant and anti-inflammatory capacity. However, its bioavailability is challenging. Therefore, food microencapsulation may be an alternative to protect polyphenols, ensuring biological effects. This study aimed to investigate the effect of a single dose of microencapsulated cocoa intake on the changes in muscle damage markers after eccentric exercise. In this randomized, double-blind, crossover design study, fourteen healthy volunteers with previous resistance training experience performed 6 x 10 maximal isokinetic eccentric contractions of the elbow flexors using an isokinetic dynamometer after ingesting 25g of microencapsulated cocoa or placebo. Peak isometric torque was measured by maximal voluntary isometric contractions and pain by visual analogic scale before, 24h, 48h and 72h after damage protocol. Plasma glutathione and malondialdehyde levels were measured using high-performance liquid chromatography, and myoglobin and C-reactive protein were determined by a fluorescence immunoassay analyzer. Significant decreases were seen in peak isometric torque and pain measures from pre to 72h post eccentric exercise. A significant main effect for time was found only for plasma myoglobin at 2h, 48h, and 72h, and 2h for C-reactive protein compared to pre values. No significant time x treatment effects were observed (all p > 0.05). This study demonstrated that microencapsulated cocoa could not improve muscle recovery after eccentric exercise, at least when consumed in a single dose.