The great green composites, the three-dimensional (3D) printing filaments containing bio-based polyester, natural hydroxyapatite and eggshell composites, were rationally designed and fabricated. We report herein novel bioactive 3D-printing filaments prepared from fish scale-derived hydroxyapatite (FHAp), polylactic acid (PLA) and a natural antibacterial agent from eggshell (EGS). The preparation of FHAp and EGS from Asian sea bass (Lates calcarifer) scales and chicken EGS, respectively, are also described. The structural, mechanical and thermal properties of the resulting composites were evaluated together with the water contact angle, free-radical scavenging ability and antibacterial effects. Polylactic acid typically exhibits poor free-radical scavenging ability and no antibacterial effect. Incorporating FHAp and EGS as fillers in the processed filament significantly enhanced the functional performance of the PLA composite. The addition of FHAp enhanced cell attachment and proliferation, suggesting osteointegration potential. The addition of EGS containing CaO component provided the antibacterial properties. PLA/EFHAp composites were porous and displayed excellent tensile strength, proliferation of mouse embryonic fibroblasts in vitro, antioxidant properties, water resistance and antibacterial properties. In addition, the developed PLA/FHAp and EFHAp filaments are amenable to large-scale production and implementation in a variety of in vivo implants of bone or other biomedical appliances.