Scaffold design remains a main challenge in tissue engineering due to the large number of requirements that need to be met in order to create functional tissues in vivo. Computer simulations of tissue differentiation within scaffolds could serve as a powerful tool in elucidating the design requirements for scaffolds in tissue engineering. In this study, a lattice-based model of a 3D porous scaffold construct derived from micro CT and a mechano-biological simulation of a bone chamber experiment were combined to investigate the effect of scaffold stiffness on tissue differentiation inside the chamber. The results indicate that higher scaffold stiffness, holding pore structure constant, enhances bone formation. This study demonstrates that a lattice approach is very suitable for modelling scaffolds in mechano-biological simulations, since it can accurately represent the micro-porous geometries of scaffolds in a 3D environment and reduce computational costs at the same time.