Bone disorders represent a significant global health burden, affecting over 200 million people worldwide and account for nearly 8.9 million fractures annually. These conditions often lead to prolonged disability, increased hospitalization, and elevated mortality, especially among the elderly that has profound impact of the economics of the nations. Bone tissue engineering using 3D porous scaffolds has emerged as a promising solution to support bone regeneration. However, conventional scaffolds face limitations such as inadequate vascularization, low mechanical strength, and insufficient stimulation of osteogenesis. To overcome these challenges, recent approaches focused on integrating bioactive ceramics like hydroxyapatite to enhance mechanical properties and angiogenic growth factors to improve vascularization and osteogenesis. In parallel, growing evidence highlights the critical role of the gut microbiota in bone health via the gut–bone axis. Notably, short-chain fatty acids (SCFAs) including acetate, butyrate, and propionate have been shown to enhance osteoblast function, suppress osteoclast activity, improve mineral absorption, and modulate systemic inflammation. This project aims to fabricate a bioactive scaffold composed of gelatin and hydroxyapatite, enriched with gut microbial SCFAs to improve osteoinductivity, biocompatibility, and bone regeneration. The scaffold will be fabricated using freeze-drying with optimized crosslinking to ensure appropriate porosity, mechanical integrity, and controlled release of SCFAs. Comprehensive physicochemical characterization, in vitro biological assays including ALP activity, mineralization, gene expression, and cytocompatibility studies, along with in vivo evaluation in rat models, will be conducted. The expected outcome is a multifunctional, metabolite-enriched scaffold capable of accelerating bone repair and offering a new paradigm in microbiota-mediated bone tissue engineering.