Due to its increased prevalence, osteoporosis (OP) represents a great challenge to health care systems and brings an economic burden. To overcome these issues, treatment plans that suit the need of patients should be developed. One of the approaches focuses on the fabrication of personalized biomaterials, which can restore the balance and homeostasis of disease-affected bone. In the presented study, we fabricated nanometer crystalline hydroxyapatite (nHAp) and iron oxide (IO) nanoparticles stabilized with APTES and investigated whether they can modulate bone cell metabolism and be useful in the fabrication of personalized materials for OP patients. Using a wide range of molecular techniques, we have shown that obtained nHAp@APTES promotes viability and RUNX-2 expression in osteoblasts, as well as reducing activity of critical proinflammatory cytokines while inhibiting osteoclast activity. Materials with APTES modified with nHAp incorporated with IO nanoparticles can be applied to support the healing of osteoporotic bone fractures as they enhance metabolic activity of osteoblasts and diminish osteoclasts’ metabolism and inflammation.