Despite a significant amount of research, the relationship between a diet rich in isoflavones and breast and prostate cancer risk is still ambiguous. The purpose of the current study was to pre-select the potential candidate for functional foods among red, white, crimson, and Persian clover sprouts, cultured for different periods of time (up to 10 days), with respect to the isoflavone content (determined by HPLC-UV-VIS), and to verify their impact on hormone-dependent cancers in vitro. The red clover sprouts were the richest in isoflavones (up to 426.2 mg/100 g dw), whereas the lowest content was observed for the crimson clover. Each species produced isoflavones in different patterns, which refer to the germination time. Hormone-insensitive MDA-MB-231 breast cancer cells were more resistant to the tested extracts than estrogen-dependent MCF7 breast cancer cells. Regarding prostate cancer, androgen-dependent LNCap cells were most susceptible to the tested sprouts, followed by androgen-insensitive, high metastatic PC3, and low metastatic DU145 cells. The observed cytotoxic impact of the tested sprouts is not associated with isoflavone content, as confirmed by chemometric analysis. Furthermore, the sprouts tested revealed a high antioxidant potential, and were characterized by high safety for normal breast and prostate cells.