Abstract Biomaterial science increasingly seeks more biomimetic scaffolds that functionally augment the native bone tissue. In this paper, a new concept of a structural scaffold design is presented where the physiological multi-scale architecture is fully incorporated in a single-scaffold solution. Hydroxyapatite (HA) and β-tricalcium phosphate (β-TCP) bioceramic scaffolds with different bioinspired porosity, mimicking the spongy and cortical bone tissue, were studied. In vitro experiments, looking at the mesenchymal stem cells behaviour, were conducted in a perfusion bioreactor that mimics the physiological conditions in terms of interstitial fluid flow and associated induced shear stress. All the biomaterials enhanced cell adhesion and cell viability. Cortical bone scaffolds, with an aligned architecture, induced an overexpression of several late stage genes involved in the process of osteogenic differentiation compared to the spongy bone scaffolds. This study reveals the exciting prospect of bioinspired porous designed ceramic scaffolds that combines both cortical and cancellous bone in a single ceramic bone graft. It is prospected that dual core shell scaffold could significantly modulate osteogenic processes, once implanted in patients, rapidly forming mature bone tissue at the tissue interface, followed by subsequent bone maturation in the inner spongy structure.