Polyether-ether-ketone (PEEK) is believed to be the next-generation biomedical material for orthopaedic implants that may replace metal materials because of its good biocompatibility, appropriate mechanical properties and radiolucency. Currently, PEEK implant represented by intervertebral fusion cage has been used successfully for many years. Till now, there is no customised PEEK orthopaedic implant made by additive manufacturing licensed for the market, although clinical trials have been increasingly reported. In this article, design criteria, including geometric matching, functional restoration, strength safety, early fixation, long-term stability and manufacturing capability, are summarised, focusing on the clinical requirements. An integrated framework of design and manufacturing processes to create customised PEEK implants is presented, and several typical clinical applications such as cranioplasty patches, rib prostheses, mandibular prostheses, scapula prostheses and femoral prostheses are described. However, the integration between Poly-ether-ether-ketone (PEEK) with hard and soft tissue represents a major challenge of PEEK orthopaedic implant owing to its chemical inertness. Here we investigated the influence of hydroxyapatite (HA) fillers and pore size of additive manufactured (AM) HA/PEEK composites scaffolds on the integration with bone and soft tissues through cellular experiments and animal experiments. The composite scaffolds were manufactured by fused filament fabrication. The cell experiment showed that the adhesion, proliferation, osteogenic differentiation and mineralization ability of mesenchymal stem cells (BMSCs) as well as the proliferation and adhesion of myofibroblasts on the PEEK/HA scaffolds were significantly improved. The in-vivo experiment demonstrated significant higher bone ingrowth and tighter adhesion of soft tissue in the HA/PEEK scaffolds. The present study provides engineering-accessible design principles on material components and geometry of AM PEEK-based composites orthopaedic implant for improving the integration with bone and soft tissue.