This paper proposes the development of a biomimetic composite based on naturally derived biomaterials. This freeze-dried scaffold contains a microwave-synthesized form of biomimetic hydroxyapatite (HAp), using the interwoven hierarchical structure of eggshell membrane (ESM) as bio-template. The bone regeneration capacity of the scaffold is enhanced with the help of added tricalcium phosphate from bovine Bone ash (BA). With the addition of Gelatin (Gel) and Chitosan (CS) as organic matrix, the obtained composite is characterized by the ability to stimulate the cellular response and might accelerate the bone healing process. Structural characterization of the synthesized HAp (ESM) confirms the presence of both hydroxyapatite and monetite phases, in accordance with the spectroscopy results on the ESM before and after the microwave thermal treatment (the presence of phosphate group). Morphology studies on all individual components and final scaffold, highlight their morphology and porous structure, characteristics that influence the biocompatibility of the scaffold. Porosity, swelling rate and the in vitro cytotoxicity assays performed on amniotic fluid stem cells (AFSC), demonstrate the effective biocompatibility of the obtained materials. The experimental results presented in this paper highlight an original biocomposite scaffold obtained from naturally derived materials, in a nontoxic manner.