Recent reports suggest that soy protein may reduce the risk of osteoporosis in peri- and postmenopausal women. The objective of this study was to examine whether soy supplementation exerts beneficial effects on serum and urinary biomarkers of bone metabolism in postmenopausal women, regardless of whether or not they are on hormone replacement therapy (HRT). A total of 71 women were randomly assigned to either soy protein (SP) or milk-based protein (MBP), 40 g daily for 3 months, in a double-blind parallel design. Forty-two women completed the study (20 on SP and 22 on MBP). Overall, both protein supplements positively influenced serum IGF-I, known to correlate with bone formation. However, SP had a more pronounced effect on IGF-I than MBP. Urinary deoxypyridinoline (Dpd) excretion, a specific biomarker of bone resorption, was significantly reduced by SP, but not by MBP when all women were included. Furthermore, women on MBP experienced a 33% increase in urinary calcium excretion, whereas SP did not have such an effect. To evaluate whether SP affects women differently on the basis of their HRT status, data from women on HRT (n = 22) and those not on HRT (n = 20) were analyzed separately. The subanalysis of the data indicated that SP had the greatest impact on serum IGF-I (an increase of 97%) in the women not on HRT. The changes in urinary Dpd due to SP were only observed in women not on HRT, indicating that the overall decrease in Dpd occurred with SP in the absence of HRT. These results indicate that soy protein may positively influence bone and calcium homeostasis in postmenopausal women, particularly those not on HRT.