Part of clinically applicable bone graft substitutes are developed by using mechanical stimulation of flow-perfusion into cell-seeded scaffolds. The role of fluid flow is crucial in driving the nutrient to seeded cells and in stimulating cell colonization. A common numerical approach is to use a multiscale model to link some physical quantities (wall shear stress and inlet flow rate) that act at different scales. In this study, a multiscale model is developed in order to determine the optimal inlet flow rate to cultivate osteoblast-like cells seeded in a controlled macroporous biomaterial inside a perfusion bioreactor system. We focus particularly on the influence of Wall Shear Stress on cell colonization to predict cell colonization at the macroscale. Results obtained at the microscale are interpolated at the macroscale to determine the optimal flow rate. For a macroporous scaffold made of interconnected pores with pore diameters of above 350 and interconnection diameters of 150 the model predicts a cell colonization of 325% after a 7-day-cell culture with a constant inlet flow rate of 0.69 . Furthermore, the strength of this protocol is the possibility to adapt it to most porous biomaterials and dynamic cell culture systems.