Ti surfaces must balance bone formation and antibacterial activity to achieve bone reconstruction and prevent infections. In this study, a Ti surface was electrochemically modified via micro-arc oxidation in an electrolyte containing calcium ions, phosphate ions, and either Ag, or Cu ions to form an antibacterial porous oxide layer on Ti surface. The resultant porous oxide layers consisted of both electrolyte and substrate elements. The Ag- and Cu-incorporated porous oxide layers exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus. Furthermore, animal experiments were performed to reveal the bone-formation on the Ag- and Cu-incorporated porous oxide layers. Both porous oxide layers promoted bone formation more effectively than untreated Ti. Thus, the Ag- and Cu-incorporated porous oxide layers formed on the Ti surface by micro-arc oxidation balanced bone formation and antibacterial activity owing to their structural and compositional features. Our findings will be useful for the surface design of Ti-based medical devices and can provide a simple electrochemical treatment to form porous surfaces to balance antibacterial activity and bone formation on Ti surfaces.