Background: Soy foods have been substituted for meat in recent years because of proposed health benefits. Research indicates, however, that soy protein and phytate in soy products inhibit the absorption of divalent cations. Methods: Our study was primarily designed to determine the effect of consuming two to three servings per day of soy foods, providing *19 g protein and *36 mg isoflavones, on iron and zinc status in premenopausal women during a 10-weeks period. As secondary outcomes, we also tested the effect of soy foods on biochemical markers of bone and thyroid hormones. Nonsmoking women (18–28 years) without chronic disease, anemia, pregnancy, or irregular menstrual cycles were randomly assigned to either the soy food (SF, n = 31) or animal food (AF, n = 32) group. Blood and urine samples and 3-day dietary records were collected at baseline and postintervention. Results: At baseline, iron and zinc status, bone markers, and thyroid hormones were not different between groups. After intervention, no significant changes were observed in hemoglobin, transferrin saturation, serum iron, ferritin, or transferrin receptor (TFR) concentrations. Plasma zinc, but not serum alkaline phosphatase, significantly decreased in both groups ( - 0.8 lmol/L). The change in bone-specific alkaline phosphatase was significant between SF (1.5 U/L) and AF ( - 0.7 U/L) groups. No significant changes were observed in bone resorption, thyroid-stimulating hormone (TSH), or free thyroxine after soy food intake. Conclusions: Incorporating *19 g soy protein from soy foods for 10 weeks had no significant effect on iron or zinc status, bone resorption or formation, or thyroid hormone status in premenopausal women.