Mandibular bone defect reconstruction remains a significant challenge for surgeons worldwide. Among multiple biodegradable biopolymers, allogeneic bone scaffolds derived from human sources have been used as an alternative to autologous bone grafts, providing optimal conditions for cell recruitment, adhesion, and proliferation and demonstrating significant osteogenic properties. This study aims to investigate the bone microstructure of the human scapula as a source for allogeneic bone scaffold fabrication for mandibular tissue engineering purposes. We created color-coded anatomical maps of the scapula and the mandible, reflecting the best anatomical and geometrical match. In this pilot study, we hypothesized a microstructural similarity of these bone structures and evaluated the human scapula’s bone tissue engineering potential for mandibular bone tissue engineering by focusing on the microstructural characteristics. Lyophilized human scapular and mandibular bioimplants were manufactured and sterilized. Experimental bone samples from the scapula’s acromion, coracoid, and lateral border from the mandibular condyle, mandibular angle, and mental protuberance were harvested and analyzed using micro-CT and quantitative morphometric analysis. This pilot study demonstrates significant microstructural qualitative and quantitative intra-group differences in the scapular and mandibular experimental bone samples harvested from the various anatomical regions. The revealed microstructural similarity of the human scapular and mandibular bone samples, to a certain extent, supports the stated hypothesis and, thus, allows us to suggest the human scapula as an alternative off-the-shelf allogeneic scaffold for mandibular reconstruction and bone tissue engineering applications.