The popular South African herbal tea, honeybush, is made from several Cyclopia species (family: Fabaceae), amongst them Cyclopia genistoides. Phytoestrogenic potential of C. genistoides. has been recently reported, however bioactivity-guided isolation of compounds with estrogenic activity has not yet been performed. A transgenic plant system, Arabidopsis thaliana pER8:GUS, was used to assay the estrogen-like activity of C. genistoides. The quantitative determination of the active compounds in the fermented and non-fermented plant material was performed by HPLC. Subsequent bioactivity-guided fractionation led to the isolation of genistein, naringenin, isoliquiritigenin, luteolin, helichrysin B and 5,7,3′,5′-tetrahydroxyflavanone, four of them first reported in the genus. Helichrysin B, naringenin and 5,7,3′,5′-tetrahydroxyflavanone differed in quantity in the fermented and unfermented herbs, the fermented plant material contained two compounds with substantial estrogenic-like activity in higher concentration (naringenin and 5,7,3′,5′-tetrahydroxyflavanone), whereas the less active helichrysin B was more abundant in the unfermented herb. The fractions as well as compounds inhibited the growth of human cancer cell lines A2780 and T47D. These results underline the phytoestrogenic activity of C. genistoides and support the rationale to the fermentation process.