Health benefits of soy isoflavones have attracted the concern of the public and the interest of health-care professionals. In this study, two trials were conducted in characterizing bone-related traits and lens proteins as affected by supplementation of soy aglycon isoflavones (SAI). In trial 1, an in vivo study, 20 Sprague-Dawley rats were ovariectomized (OVX) and randomly distributed into OVX and OVX+SAI (135 mg of SAI/kg of feed; 8.33 mg/kg body weight; 2.5 mg/day) groups. Another group containing 10 rats with a sham operation was control (Sham). The experiment period was 3 months, and the rats were subjected to bone-related traits and lens protein characterization. In trial 2, an in vitro study, osteoprogenitor cells (UMR-106) were divided into SAI-supplemented (0.5 mg of SAI/mL of medium) and unsupplemented groups. Results of the in vivo study indicated that daily BW gains in the OVX and OVX+SAI groups were greater than that of the Sham group (p < 0.05). Bone ash and Ca contents of the Sham and OVX+SAI groups were higher than those of the OVX group (p < 0.05), while bone density, strength, and phosphorus contents among groups varied insignificantly (p > 0.05). When the lens proteins were extracted and analyzed with size-exclusion HPLC, the contents of beta- and gamma-crystallins were lowest in the OVX group and the protein solubility decrease could be recovered by dietary SAI supplementation (shown by OVX+SAI group). Based on Raman spectra of the isolated lens proteins, disulfide bonds were observed more in OVX lens than in the Sham and OVX+SAI lens. Results of in vitro study with osteoprogenitor cells revealed that cell viability, alkaline phosphatase activity, osteocalcin, and Ca contents of the SAI-supplemented group were higher than those of the unsupplemented group (p < 0.05). The likely potency to enhance bone and lens health by SAI supplementation is worth pointing out.