Polyetheretherketone (PEEK) is a widely used engineering plastic in orthopedic and dental implants, but its bioinertness leads to poor bone integration. To overcome this, a sulfonation treatment was applied to PEEK first to create a rough, microporous surface enhancing cellular adherence and integration. Subsequently, amorphous magnesium phosphate (AMP) nanosheets were produced through microwave-assisted synthesis, and hydroxyapatite (HA) was generated using a bionic solution hydrothermal method. A dual-layer coating system composed of an interlayer AMP and a top layer HA on the surface of PEEK was developed to enhance osteointegration. Surface analysis confirms the creation of increased surface area, improved hydrophilicity with introduced hydrophilic groups, and enhanced protein attraction. In vitro assessments on mouse embryonic osteoblasts (MC3T3-E1) demonstrate the non-toxicity of these coatings and their efficacy in promoting cell proliferation. Moreover, antimicrobial evaluations against E. coli and S. aureus highlight the potential of these composite coatings in preventing implant-related infections. The AMP/HA dual-layer coating on sulfonated PEEK emerges as a potent method for enhancing osteointegration and antibacterial properties, offering a promising approach to improve bone repair efficiency in clinical applications.