Peri-implantitis is characterized by inflammation resulting from bacterial infections in peri-implant connective tissue. The purpose of this study was to prepare and characterize chitosan/gelatin (CSG)-based membranes with antibacterial agents to functionalize the surface of titanium (Ti) implants. CSG membranes were prepared on Ti substrates via electrophoretic deposition (EPD). Quercetin, an active flavonoid responsible for fulfilling various plant functions, was introduced as an antibacterial agent to be loaded into the membrane during preparation. The fabrication of quercetin-loaded CSG membranes via EPD was also investigated. Fluorescent microscope, Attenuated Total Reflection Fourier transform infrared spectroscopy, and X-ray diffraction results verified the entrapment of quercetin. The membranes swelled by 150% of mass after rehydration. The antibacterial effects of quercetin on Gram-positive bacteria, such as Staphylococcus aureus and methicillin-resistant Staphylococcus aureus, were verified by spread-plate, scanning electron microscopy, and live/dead staining. Cytological experiments showed that the biocompatibility of rat bone marrow mesenchymal stromal cells was promoted by quercetin-loaded membranes, exclusively in the group with the highest content of quercetin. The quercetin-loaded groups also enhanced the antineoplastic activity of MG-63 cells. These results suggested that quercetin-loaded CSG membranes were successfully fabricated via EPD. Thus, biocompatible and antibacterial membranes could be a potential strategy to functionalize Ti implants.