Accurate prediction of transverse shear deformation is essential for the serviceability assessment, durability-oriented design, and structural health monitoring of hybrid and heterogeneous beam members. This is particularly relevant for lightweight composite components in which a porous cementitious matrix (e.g., perlite-based material) is combined with an embedded steel I-section, yielding strong stiffness contrasts and spatially nonuniform shear transfer. In this study, an energy-consistent analytical–numerical framework is proposed to determine the effective shear correction factor ks for such non-homogeneous cross-sections within the Timoshenko beam theory. The formulation enforces equivalence between the real heterogeneous shear strain energy, governed by a spatial shear modulus field G(y,z), and its beam-theory representation based on ks(Gref A). A pixel/voxel discretization is introduced to evaluate the generalized shear-energy integral and to quantify the deviation of ks from classical homogeneous benchmarks. The results demonstrate that shear stiffness may be controlled by localized energy concentrations near weak matrix regions and phase interfaces, which can lead to non-negligible errors in deflection predictions when standard shear correction factors are adopted. The proposed framework provides a transparent and computationally efficient tool to support reliability-driven stiffness identification, model updating, and health monitoring strategies for heterogeneous and hybrid beam components.