In this study, the aim was to investigate the changes in the physical, chemical and biological properties of chitosan scaffolds obtained by freeze-drying and microwave-assisted gas foaming methods. Also, it was aimed to determine the most suitable one when scaffolds are subjected to different stabilization processes. To prevent the solubility of chitosan scaffolds, stabilization processes were carried out by treatment with ethanol (EtOH), sodium hydroxide (NaOH), or sodium bicarbonate (Na2CO3). The chemical and physical changes in the chitosan structure induced by different stabilization methods were investigated by characterization studies carried out comparatively with two-dimensional chitosan films. The results showed that, particularly, NaOH stabilization improved the physical, thermal, and mechanical properties of the bulk material. The wettability and surface roughness of the chitosan films were enhanced for cellular adhesion after stabilization. Cell culture studies revealed that variations in both fabrication and stabilization methods significantly affected in vitro cellular responses such as cell attachment, proliferation and viability. In conclusion, chitosan scaffolds fabricated by microwave-assisted gas foaming and stabilized by NaOH solution were found as the best structure due to their higher cellular activities.