Polyetheretherketone (PEEK) is a high-performance thermoplastic biomaterial which is currently used in a variety of biomedical orthopaedic applications. It has comparable tensile and compressive strength to cortical bone with favourable biocompatibility. However, natural grade PEEK-OPTIMA has shown insufficient bioactivity and limited bone integration. Bioactive PEEK composites (e.g., PEEK/calcium phosphates or Bioglass) and porous PEEK have been used to improve bone-implant interface of PEEK-based devices, but the bioactive phase distribution or porosity control is poor. In this paper, a novel method is developed to fabricate a bioactive PEEK/hydroxyapatite (PEEK/HA) composite with a unique configuration in which the HA (bioactive phase) distribution is computer-controlled within a PEEK matrix. This novel process results in complete interconnectivity of the HA network within a composite material, representing a superior advantage over alternative forms of product. The technique combines extrusion freeforming, a type of additive manufacturing (AM), and compression moulding. Compression moulding parameters, including pressure, temperature, dwelling time, and loading method together with HA microstructure were optimized by experimentation for successful biocomposite production. PEEK/HA composites with a range of HA were produced using static pressure loading to minimise air entrapment within PEEK matrix. In addition, the technique can also be employed to produce porous PEEK structures with controlled pore size and distribution.