Elastic modulus and strength of trabecular bone are negatively affected by osteoporosis and other metabolic bone diseases. Micro-computed tomography-based beam models have been presented as a fast and accurate way to determine bone competence. However, these models are not accurate for trabecular bone specimens with a high number of plate-like trabeculae. Therefore, the aim of this study was to improve this promising methodology by representing plate-like trabeculae in a way that better reflects their mechanical behavior. Using an optimized skeletonization and meshing algorithm, voxel-based models of trabecular bone samples were simplified into a complex structure of rods and plates. Rod-like and plate-like trabeculae were modeled as beam and shell elements, respectively, using local histomorphometric characteristics. To validate our model, apparent elastic modulus was determined from simulated uniaxial elastic compression of 257 cubic samples of trabecular bone (4 mm×4 mm×4 mm;​ 30 μm voxel size;​ BIOMED I project) in three orthogonal directions using the beam–shell models and using large-scale voxel models that served as the gold standard. Excellent agreement (R²=0.97) was found between the two, with an average CPU-time reduction factor of 49 for the beam–shell models. In contrast to earlier skeleton-based beam models, the novel beam–shell models predicted elastic modulus values equally well for structures from different skeletal sites. It allows performing detailed parametric analyses that cover the entire spectrum of trabecular bone microstructures.