Scaffolds are often designed with progressive degradation to make way for cell proliferation of seeded cells for native tissue. The viability of the scaffold has been shown to depend on, among other things, the microstructure. Common parameters, that are used to describe microstructure, are porosity, material thickness, pore size and surface area. These properties quantify the suitability of the scaffold as a substrate for cell adhesion, fluid exchange and nutrient transfer. Bone and cartilage scaffolds are often placed or operated under loads (predominantly compression). This can alter the structural parameters depending on the stiffness of the scaffold and applied deformation. It is important to know, how scaffolds’ parameters change under deformation. In this study, two scaffolds (PLCL-TCP and collagen-PLA) intended for use in bone and cartilage applications, were studied through micro computed tomography based imaging and in situ mechanical testing. The scaffolds were subjected to uniaxial compressive deformation up to 50% of the original size. The corresponding changes in the individual scaffold bulk characteristics were analyzed. Our results show an expected decrease in porosity with increasing deformation (with PLCL-TCP scaffold 52% deformation resulted in 56% decrease in porosity). Especially in the sandwich constructs of collagen-PLA, but also in PLCL-TCP composites, it was evident that different materials are affected differently which may be of significance in applications with mechanical loading. Our results are a step towards understanding the changes in the structure of these scaffolds under loading.