Recent advances in the solid-liquid extraction have brought a large number of new techniques as ultrasonic assisted extraction (UAE). Different solvents such as alcohols, acetonitrile and chloroform are reported as extractors of added-value compounds. Ionic liquids (ILs) have been used the last few years as a non- conventional solvent for the extraction of alkaloids from natural sources. This work aims to extract efficiently alkaloids such as Caffeine (CF) and Theobromine (TB) from cacao, using protic ionic liquids (PILs) based onultrasonic assisted extraction (PIL-UAE). In order to optimize the extraction, a 23 factorial design was appliedusing three parameters (extraction time, ratio of mass/volume, solvent concentration). The extraction method was applied to cacao seeds, using 2-hydroxy ethylammonium acetate (2HEAA) as PIL. The results indicated that protic ionic liquids showed remarkable effects on the extraction yields of alkaloids. The main variable that influences the extraction process of the alkaloids is the solid / liquid ratio; however, the ultrasonic power has no effect.