To date, no studies have exploited micro-CT in humans to evaluate bone morphology and structure after bone augmentation with CAD/CAM-customized titanium mesh, in mandible and maxilla. The aim of this study was to assess the composition and microstructure of bone biopsy through micro-CT analysis. Bone augmentation at both maxillary and mandible sites was performed on 30 patients randomly treated with customized mesh, either alone (M-) or covered with resorbable membrane (M+), in both cases filled 50:50 with autogenous bone and xenograft. After 6 months, biopsies were taken and micro-CT was performed on consecutive 1-mm-thick VOIs from coronal to apical side, measuring tissue volumes, trabecular thickness, spacing, and number. In both groups, irrespective of membrane use, bone tissue (M-: 29.76% vs. M+: 30.84%) and residual graft material (M-: 14.87% vs. M+: 13.11%) values were similar. Differences were site-related (maxillary vs. mandibular) with higher percentage of bone tissue and trabecular density of low-mineralized bone and overall bone in the mandible. The composition and structure of bone tissue, as assessed by micro-CT after alveolar ridge augmentation using CAD/CAM-customized titanium meshes, showed similar features regardless of whether a collagen membrane was applied.