Few studies investigated the effects of nutrition education and exercises in women with osteopenia. This study examined the relationship between changes in dietary intakes and changes in indicators related to bone health in postmenopausal women with osteopenia (-2.5 ${leq}$ T-score ${leq}$ 1) after a 12-week intervention. Thirty-one postmenopausal women aged > 50 years residing in Seoul were recruited and participated in nutritional education regarding bone health and general nutrition practices and aerobic exercises (three times a week; 60 min per session). Twenty-five subjects completed the study and were eligible for the analysis. Bone mineral density (BMD) at femoral neck was measured by dual energy x-ray absorptiometry. Serum calcium, osteocalcin, and intact parathyroid hormone (PTH) were also measured. Dietary intake was estimated by using a one-day 24 recall by a clinical dietitian. After 12 weeks, meat consumption increased (P = 0.028) but vegetable intake decreased (P = 0.005). Intakes of animal protein (P = 0.024), vitamin B1 (P = 0.012) and vitamin $B_2$ (P = 0.047) increased, and sodium intake decreased (P = 0.033). Intact PTH (P = 0.002) decreased and osteocalcin (P = 0.000) increased, however, BMD decreased (P = 0.000). Changes in mushroom consumption were positively correlated with femoral neck BMD (r = 0.673, P = 0.003). Changes in animal iron intake were negatively correlated with intact PTH (r = -0.488, P = 0.013) but were positively correlated with osteocalcin (r = 0.541, P = 0.005). These results suggested that the association between animal iron intake and biochemical markers of bone turnover may play an important role in bone metabolism. Further studies are needed to shed light on complicated mechanisms of diet, hormonal levels of bone metabolism, and bone density.