Background: Pueraria candollei var.mirifica (PC) is a tuberous plant enriched with bioactive phytoestrogens. PC is currently high demanded in the global markets as dietary supplement products, which resulted in a shortage of tuberous root from the natural resource and the field cultivation. Materials and Methods: We compare phytoestrogens contents from the tuberous root and stem of PC and their estrogenic activities on MCF-7 cells proliferation. Results: The root and stem of PC accumulated different contents of phytoestrogens. The highest amount of total isoflavonoids and total chromenes was found in the root bark of PC. However, the stem bark (10 μg/mL crude extract) which contains a high level of chromenes and low amount of isoflavonoids exhibited higher growth stimulation of MCF-7 cells (127.25% ± 4.43% relative proliferative effect [RPE] as compared to estradiol [10−10 M]) than root bark at the same concentration with 116.32% ± 3.59% RPE. After the solubilization of the ethanol extract with 10% (v/v) aqueous ethanol, the soluble fraction of crude extract of stem stimulated proliferation of MCF-7 cells without cell growth suppression effect at high concentration (100 μg/mL) as observed in the insoluble fraction of the extract. Conclusion: We suggested that the soluble part of crude extract might be less toxic than the ethanolic crude extract and its non-polar components. Our study opens the possibility of using the stem of PC as a new alternative source of bioactive phytoestrogens for dietary supplement products.