Micro-computed tomography (Micro-CT) is an excellent method to analyze the internal architecture of tissue engineering scaffolds in a 3D and non-destructive fashion. The acquisition parameters have a vital role in the entire analysis process. There is no consensus on the optimal acquisition parameters for tissue engineering scaffolds. There is a wide range of used acquisition parameters in the literature without justification. The aim of the study is to identify the effects of the scanning parameters on the final results (e.g. porosity, mean pore size and mean wall thickness) of different polymeric (e.g. silk fibroin) and ceramic (hydroxyapatite) scaffolds for application in tissue engineering strategies.