In this work, we demonstrated that MRI combined with appropriate contrast agents is an advantageous tool to investigate the physical properties of materials. In particular, we used this approach to examine the diffusion and perfusion properties of porous bio-compatible materials (i.e. scaffolds) commonly used to develop 3D cell culture models. Thanks to the deuterium's different spin number compared to the hydrogen one, we submerged water-filled scaffolds into an enclosed container filled with deuterium oxide (D 2 O). Hence, we imaged, over time, the diffusion of water molecules enclosed in scaffolds into the surrounding environment. Furthermore, microfluidics and custom-made meshes were crucial to study the perfusion properties of such materials, highlighting the importance of the scaffold stiffness, density and porosity type. Therefore, we show a novel methodology to effectively study diffusion and perfusion in a fast, easy, low-cost and reproducible way.