Favelines, benzocycloheptene diterpenes exclusively found in Cnidoscolus quercifolius, have shown promising anticancer properties, particularly phyllacanthone. Nevertheless, the isolation of these compounds remains challenging due to their similar polarity. The use of centrifugal partition chromatography (CPC) has enabled the quick and efficient purification of phyllacanthone from C. quercifolius crude extract with a yield of 4.5% (w/w) and a purity of 83%. Favelines-enriched fractions were also obtained and purified by preparative HPLC, resulting in the isolation of faveline, isofavelol, and deoxofaveline. In addition, phyllacanthone B, a previously unreported derivative, was identified and characterized. Pharmacological evaluations revealed the significant anti-melanoma activity of purified metabolites, with distinct structure-activity relationships. These results shed light on the mechanism of action of favelines, suggesting their potential as hits for the development of novel anticancer agents.