Plant genotypes and processing technologies affect health properties of foods. How thermal processes with different sterilization values influence polyphenols in soymilk manufactured from different genotypes, particularly black soybean has not been well characterized. This study's aims were to investigate how one- and two-phase ultrahigh temperature (UHT) processing technologies, with wide differences of lethality (F0 158.5 and 6.35, respectively), affected anti-prostate cancer DU145-cell properties of black soymilk compared to light-yellow-Proto soymilk. Phenolics were extracted from soymilk and used for chemical, cell cycle and apoptosis analyses. Total isoflavones and genistein in black soymilk were significantly higher than Proto soymilk by either processing methods. Compared to one-phase processing, two-phase produced higher gallic acid in both soybeans, and higher oxygen radical absorbance capacity (ORAC) in black soymilk. Soymilk processed from both genotypes by both UHT methods inhibited DU145 cells. Two-phase-UHT processed black soymilk was more effective than one-phase UHT-processed soymilk. IC50 values (mg/mL) of black and yellow soy extracts against prostate cancer cells differed only by 11%-25%, which were lower than the differences of total isoflavone (29%-33%) or genistein (>50% between two beans). The mechanism by which soymilk inhibited DU145 cell proliferation was through apoptosis as evidenced by cell cycle analyses and expressions of caspase-3, Bcl-2, and PARP-1 proteins. Antioxidant properties, isoflavones, and phenolic acids were negatively correlated with prostate-cancer-cell inhibition IC50 (p<0.05) with ORAC having the highest coefficient (r=-0.98). Overall, two-phase-UHT processing of soybean would produce soymilk products with a higher health benefit than a one-phase UHT method. PRACTICAL APPLICATION: This study characterized the potential prostate cancer prevention effect of soymilk's phenolic extract in black soybean and compared with yellow soybean. The crude extract can be prepared much less costly than purified isoflavones and has potential to be developed into a dietary supplement. This study shows differences of soymilks made by continuous high-temperature processing of two soybean types and can serve as a scientific foundation for future clinical research and commercialization.