Additive Manufactured (AM) Polyether-ether-ketone (PEEK) orthopaedic implants offer new opportunities for bone substitutes. However, owing to its chemical inertness, the integration between PEEK implants and soft tissue represents a major challenge threatening the early success of the PEEK implants. Here we investigated the influence of hydroxyapatite (HA) fillers and porous structure of AM HA/PEEK scaffolds on the integration with soft tissue through in-vitro cellular experiments and in-vivo rabbit experiments. Among the animal experiments, HA/PEEK composite scaffolds with HA contents of 0, 20 wt%, 40 wt% and pore sizes of 0.8 mm, 1.6 mm were manufactured by fused filament fabrication. The results indicated that HA promoted the proliferation and adhesion of myofibroblasts on PEEK-based composites by releasing Ca2+ to active FAK and its downstream proteins, while the surface morphology of the scaffolds was also roughened by the HA particles, both of which led to the tighter adhesion between HA/PEEK scaffolds and soft tissue in-vivo. The macroscopic bonding force between soft tissue and scaffolds was dominated by the pore size of the scaffolds but was hardly affected by neither the HA content and nor the surface morphology. Scaffolds with larger pore size bonded more strongly to the soft tissue, and the maximum bonding force reached to 5.61 ± 2.55 N for 40 wt% HA/PEEK scaffolds with pore size of 1.6 mm, which was higher than that between natural bone and soft tissue of rabbits. Although the larger pore size and higher HA content of the PEEK-based scaffolds facilitated the bonding with the soft tissue, the consequent outcome of reduced mechanical properties has to be compromised in the design of the porous PEEK-based composite implants. The present study provides engineering-accessible synergistic strategies on material components and porous architecture of AM PEEK orthopaedic implants for improving the integration with soft tissue.