Despite recent years' remarkable progress in medical procedures for bone reconstruction, the implementation of newly developed biomedical materials is still facing technical drawbacks, such as, lack of mechanical strength, impaired cellular proliferation and differentiation, limited osteogenesis and issues related to bone infection, osseointegration and vascularization in large defects.This paper presents a methodology to predict the potential behaviour of bioceramic-based composite scaffolds for bone engineering applications, based on the evaluation of its morphological features, mechanical properties, and mechanical stimulus' input to cells. Chitosan/biphasic calcium phosphates (CH/BCP) composite scaffolds with different structural parameters, namely pore size, filament thickness and layer overlapping, pore size gradient and irregularity on the filament positioning were considered. The finite element simulation was validated against experimental results on 3D printed scaffolds, being proposed an in silico model for the characterization of the scaffolds' material composition. With this study, the influence of the CH/BCP bulk material mechanical properties on the scaffolds mechanical behaviour was demonstrated. CH/BCP show to behave according to a Yeoh hyperelastic material model. Scaffolds with a regular structure and 500 μm filament distance (PL500) or irregular architecture models (IS2 scaffold) demonstrated better equilibrium among the analysed features, namely to promote cell adhesion and migration, nutrient and oxygen flow, vascularization, mechanical capacity to support the load without experiencing premature failure and initial bone formation through the transmission of bone growth mechanical stimulus. A good correlation between this study and literature data was obtained, which highlighted the suitability of the proposed methodology to infer on the scaffold biomechanical behaviour and allowing the scaffold improvement at an early stage of conceptualization.