Plant-derived phytoestrogens are considered to be an alternative therapy for the prevention and control of bone loss in postmenopausal women. However, there are contradictory findings among clinical studies in the efficacy of soy isoflavones on bone metabolism in postmenopausal women. Inter-individual differences in gut bacteria metabolism of isoflavones to produce equol (the equol-producing phenotype) might partly explain these discrepancies. Among several trials in this area of research, few studies took the equol-producing phenotype into consideration, and those studies support the importance of this phenotype in the effect of soy isoflavones on bone health among post-menopausal women. Greater consideration of the equol-producing phenotype in the design of studies investigating the effect of soy isoflavones on bone health of postmenopausal women may provide more useful information.