Immobilized silver nanoparticles (Ag NPs) can give titanium contact-killing action against the colonization of bacteria. However, this antimicrobial process may produce bacterial debris, which is likely to compromise the osteogenic property of the material. Magnesium, as an effective stimulus for boosting the osteogenic performance of bone cells, may neutralize this adverse impact. Accordingly, the present study illuminates the effect of bacterial debris (BD) and lipopolysaccharide (LPS, a kind of endotoxin in microbial debris) on the osteogenesis of titanium, which was surface-modified by magnesium (Mg) and/or silver (Ag) plasmas. It was found that the unfavorable effects of LPS and BD on osteoblastic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) can be overcome by doping with magnesium on the titanium surface. And titanium co-doped with magnesium and silver, even under the challenge of bacteria, gives the best osseointegration in vivo. This study highlights that bacterial debris can impair the osseointegration of implants and co-doping by magnesium and silver is a promising method to solve this issue.