Cocoa and its products are rich sources of polyphenols such as flavanols. These compounds exert antioxidant and anti-inflammatory activities, accountable for cocoa health-promoting effects. However, cocoa polyphenols are poorly absorbed in the intestine, and most of them cannot reach the systemic circulation in their natural forms. Instead, their secondary bioactive metabolites are bioavailable, enter the circulation, reach the target organs, and exhibit their activities. In fact, once reaching the intestine, cocoa polyphenols interact bidirectionally with the gut microbiota. These compounds can modulate the composition of the gut microbiota exerting prebiotic mechanisms. They enhance the growth of beneficial gut bacteria, such as Lactobacillus and Bifidobacterium, while reducing the number of pathogenic ones, such as Clostridium perfringens. On the other hand, bioactive cocoa metabolites can enhance gut health, displaying anti-inflammatory activities, positively affecting immunity, and reducing the risk of various diseases. This review aims to summarize the available knowledge of the bidirectional interaction between cocoa polyphenols and gut microbiota with their various health outcomes.