Although polyetheretherketone (PEEK) has been considered as a potential orthopedic and dental application material due to its similar elastic modulus as bones, inferior osseointegration and bacteriostasis of PEEK hampers its clinical application. In this work, fluorinated PEEK was constructed via plasma immersion ion implantation (PIII) followed by hydrofluoric acid treatment to ameliorate the osseointegration and antibacterial properties of PEEK. The surface microstructure, composition, and hydrophilicity of all samples were investigated. Rat bone mesenchymal stem cells (rBMSCs) were cultured on their surfaces to estimate bioactivity. The fluorinated PEEK can enhance the cell adhesion, cell spreading, proliferation, and alkaline phosphatase (ALP) activity compared to pristine PEEK Furthermore, the fluorinated PEEK surface exhibits good bacteriostatic effect against Porphyromonas gingivalis, which is one of the major periodontal pathogens. In summary, we provide an effective route to introduce fluorine and the results reveal that the fluorinated PEEK can enhance the osseointegration and bacteriostasis, which provides a potential candidate for dental implants.