Quality assessment of cocoa-based food products (i.e., chocolate) reached increasing interest by scientific research, as it is rich in bioactive compounds (BCs) (i.e., catechins, methylxanthines, serotonin, etc.), which can have beneficial effects on human health (cardiovascular, immunomodulatory, mood regulator, etc.). Thus, the cocoa content may influence the quality of chocolate products. In this regard, the study aimed at a comprehensive evaluation of different BCs: biogenic amines (BAs), free fatty acids (FFAs), and antioxidant compounds (Total Polyphenols Content, TPC and Antioxidant Activity, AA), in chocolate samples with different cocoa contents (50%, 60%, 70%, 85%, 100%). By means of HPLC-UV/RF analysis, chocolates samples with higher cocoa content showed the highest concentration of serotonin, which represented the 25% of the total BAs concentration. Considering the total FFAs, unsaturated fatty acids (linoleic, linolenic and oleic) accounted for 30 to 50% in all chocolate samples analyzed. Antioxidant assays showed a great variability within samples, mainly highlighting a gradual increase of TPC and AC as a function of higher cocoa content. The findings of this study provide useful insights into cocoa-based products, showing that cocoa content influences the BCs concentration, thus improving the nutritional characteristics and the quality of the final product.