Peri-implant lesions, such as peri-implant mucositis and peri-implantitis, are bacterial-derived diseases that happen around dental implants, compromising the long-term stability and esthetics of implant restoration. Here, we report a surface-modification method on zirconia implant abutment using silver linear-beam ion implantation to reduce the bacterial growth around the implant site, thereby decreasing the prevalence of peri-implant lesions. The surface characteristics of zirconia after ion implantation was evaluated using energy dispersive spectroscopy, X-ray photoelectron spectroscopy, and a contact-angle device. The antibacterial properties of implanted zirconia were evaluated using Streptococcus mutans and Porphyromonas gingivalis. The biocompatibility of the material surface was evaluated using human gingival fibroblasts. Our study shows that the zirconia surface was successfully modified with silver nanoparticles by using the ion-implantation method. The surface modification remained stable, and the silver-ion elution was below 1 ppm after one-month of storage. The modified surface can effectively eliminate bacterial growth, while the normal gingiva’s cell growth is not interfered with. The results of the study demonstrate that a silver-ion-implanted zirconia surface possesses good antibacterial properties and good biocompatibility. The surface modification using silver-ion implantation is a promising method for future usage.