Soy protein is reported to prevent bone loss in both women and rat models of osteoporosis. However, the role of soy isoflavones on the trabecular microarchitectural properties needs to be explored. In the present study, we examined whether soy protein with graded doses of isoflavones reverses loss of bone mineral density (BMD), bone mineral content (BMC), and trabecular microstructure in an ovariectomized (Ovx) osteopenic rat model. Seventy-eight 9-m old female Sprague-Dawley rats were either sham-operated (Sham; 1 group) or Ovx (5 groups) and fed a semi-purified casein-based diet. After 90 days, the occurrence of bone loss was confirmed using dual energy X-ray absorptiometry. Thereafter, rats were assigned to the following treatments: Sham, Ovx (control), Ovx + 17beta-estradiol (E(2); 10 microg/kg body wt. twice per week), Ovx + soy protein depleted of isoflavones (Soy-; 0.06 mg isoflavones/g protein), Ovx + soy protein with normal isoflavone content (Soy; 3.55 mg isoflavones/g protein), and Ovx + isoflavone-enriched soy protein (Soy+; 7.10 mg isoflavones/g protein). After 125 days of treatment, rats were euthanized, and tibia and lumbar bones were collected for the assessment of BMD, BMC, and trabecular microarchitectural properties using X-ray microcomputed tomography. None of the treatments had an effect on BMD or microarchitectural properties of the lumbar vertebra. However, Soy treatment significantly increased tibial BMC and BMD by 10% and 4.5% compared with Ovx control, but the increase in BMD was not enough to reach the BMD levels of the Sham control group. The Soy+ diet positively affected the tibial architectural properties including trabecular thickness, separation, and number. In summary, our findings suggest that soy protein does not restore bone loss in osteopenic rats; however, higher doses of isoflavones may be required to reverse the loss of tibial microstructural properties.