One of the most common prophylactic techniques to solve prosthetic joint infection (PJI) is incorporation of antibiotics into acrylic bone cement to prevent bacterial colonization and proliferation by providing local antibiotic delivery directly at the implant site. Further, there has been a significant concern over the efficacy of commonly used antibiotics within bone cement due to the rise in multi-drug resistant (MDR) microorganisms. Selenium is an essential trace element that has multiple beneficial effects for human health and its chemotherapeutic action is well known. It was reported that nanostructured selenium enhanced bone cell adhesion and has an increased osteoblast function. In this context, we used the selenium nanoparticles (SeNPs) to improve antibacterial and antioxidant properties of poly (methyl methacrylate) (PMMA) and tri calcium phosphate (TCP)-based bone cements, and to reduce of the infection risk caused by orthopedic implants. As another novelty of this study, we proposed phosphatidylcholine (PC) as a unique and natural stabilizer in the synthesis of selenium nanoparticles. After the structural analysis of the prepared bone cements was performed, in vitro osteointegration and antibacterial efficiency were tested using MC3T-E1 (mouse osteoblastic cell line) and SaOS-2 (human primary osteogenic sarcoma) cell lines, and S. aureus (Gram positive) and E.coli (Gram negative) strains, respectively. More importantly, PC-SeNPs-reinforced bone cements exhibited significant effect against E. coli, compared to S. aureus and a dose-dependent antibacterial activity against both bacterial strains tested. Meanwhile, these bone cements induced the apoptosis of SaOS-2 through increased reactive oxygen species without negatively influencing the viability of the healthy cell line. Furthermore, the obtained confocal images revealed that PC-SeNPs (103.7 ± 0.56 nm) altered the cytoskeletal structure of SaOS-2 owing to SeNPs-induced apoptosis, when MC3T3-E1 cells showed a typical spindle-shaped morphology. Taken together, these results highlighted the potential of PC-SeNPs-doped bone cements as an effective graft material in bone applications.