Capsaicin is a very powerful alkaloid with important pharmacological effects and pain relief additives. It also aids in cancer prevention and weight reduction, among others benefits. New and promising techniques based on microwave-assisted and aqueous two-phase systems are considered “green techniques” for extraction and purification of bioactive compounds. This work discusses an integrated process of extraction and purification of capsaicin from biomass Capsicum chinense var. cumari-do-Para by a microwave-assisted method followed by aqueous two-phase systems (ATPS) based on ethanol + sodium salts. The diagram phases of ATPS were complete characterized and the ability of the salts to promote the formation of ATPS with ethanol follows this trend: NaH 2 PO 4 2 S 2 O 3 2 SO 4 2 CO 3 . Using the optimized conditions, the capsaicin from its natural source, was purified around 5.2-fold with an extraction efficiency of ≈85.6% for the ethanol-rich phase, and DPPH radical inhibition capacity of ≈80%.