Flavanols-rich cocoa has positive effects on lipid metabolism and might enhance the performance of athletes through an improvement in their body composition. To test this hypothesis a placebo-controlled intervention study in training endurance athletes who received 5 g of cocoa daily (425 mg of flavanols) for 10 weeks was performed. Dietary intake, body composition, exercise performance and plasma levels of follistatin, myostatin and leptin were measured. Cocoa intake significantly reduced body fat percentage (p = 0.020), specifically in the trunk (p = 0.022), visceral area (p = 0.034) and lower limbs (p = 0.004). The reduction in body fat mass was accompanied by an increase in plasma follistatin and a decrease in leptin, while myostatin levels remained unchanged. The intake of cocoa reduced the percentage of body fat of athletes, without any impact on athletes’ performance. The change in fat body composition did not improve athletes’ performance.