Roasting and fermentation are key steps in cocoa processing that can be modulated to optimize the presence of health-promoting compounds in the final product. Roasting promote melanoidins formation and polyphenols depolymerization. Results of Forastero and Criollo cocoa beans were processed in different conditions showed that higher fat content and high phenolic content could promote melanoidins formation. Forastero variety had the highest melanoidins and phenols concentration under severe roasting conditions. More severe thermal treatment decreased the concentration of total phenolic compounds and proanthocyanidins in both varieties and also influenced the flavan-3-ols profile. The antioxidant activity determined using DPPH Quencher assay was the highest in Forastero fractions above 20 kDa obtained under severe roasting condition; thus supporting the idea that melanoidins play a major role in roasted cocoa antioxidant activity. It can be concluded that a proper design of roasting process and the adequate selection of cocoa variety can optimize the cocoa health potential; especially melanoidins and phenolic compounds.