Changes in functional compounds and antioxidant capacity during processing were investigated in cocoa beans, and the sensory profile of cocoa paste was determined. 97 cocoa samples were collected from Tingo María (TM), 17 from San Alejandro (SA) and 21 from Curimana (CU), in Peru. The content of total phenolic compounds in fresh grains differed between areas. The highest antioxidant capacity was found in fresh grains GCZfres, CM4fres and OC2fres. The GCZ9li cocoa paste sample had the lowest anthocyanin content. Antioxidant capacity was mainly influenced by phenols, followed by anthocyanins and reducing sugars. OC2 cocoa paste had a distinctive cocoa flavor, while GCZ9 had an intense cocoa flavor with fruity notes and marked acidity, and CMA4 had a similar but less intense flavor than OC2.