By using Layer-by-Layer (LbL) assembly, micro- and nano-scale coatings can be applied to porous structures, allowing for the potential customisation of scaffolds for bone tissue engineering applications. In this study, we developed a purpose-designed LbL assembly system, enabling continuous perfusion flow and cyclic compression, to fabricate LbL multilayer-coated scaffolds with tailored properties. Their physicochemical properties were analysed using SEM and FTIR spectroscopy, while their elastic compressive modulus quantified their mechanical performance. This study compared immersion alone (i.e., static conditions) to the combination of perfusion flow (12 mL min−1, 10 rpm) and cyclic compressive loading (5% strain, 1 Hz) (i.e., dynamic conditions) as methods to influence coating deposition during LbL assembly. The results demonstrated that the LbL-coated scaffolds with 40-multilayer coatings deposited under dynamic conditions demonstrated a 40-fold improvement in the compressive elastic modulus compared to uncoated scaffolds and a 16-fold increase was achieved when the LbL coatings were applied under static conditions. Importantly, application of the dynamic coating conditions during the LbL assembly process preserved the high porosity and interconnectivity of the scaffolds even after applying the 40-multilayer coating. Moreover, the nanocomposite coatings enhanced surface characteristics such as roughness and hydrophilicity. Taken together, adoption of the proposed approach of combining perfusion flow and cyclic compression loading during assembly of LbL-coated scaffolds is a promising approach for bone tissue engineering applications.