Structural integrity and interconnected porosity are essential design criteria for bone tissue scaffolds. This study presents the optimisation of electrostatic layer-by-layer (LbL) assembly conditions for nanocomposite multilayer coatings on highly porous polyurethane scaffold templates, relevant to bone scaffold applications. Mechanically robust LbL coatings were applied to enhance the balance between scaffold porosity and mechanical strength. A design of experiments (DoE) approach using response surface methodology (RSM) was conducted in two stages to systematically optimise both LbL process parameters and nanocomposite composition. The optimised scaffolds exhibited a 260-fold increase in elastic modulus, from 0.09 MPa (uncoated) to 23.55 MPa, while maintaining a highly interconnected pore structure with 78.2% ± 1.24 porosity. These results establish a systematic framework for tuning LbL assembly on porous scaffolds towards bone tissue engineering.