Chitosan (CHT) is a polysaccharide with multiple claimed properties and outstanding biocompatibility, generally attributed to the presence of protonable amino groups rendering a cationic natural polymer. However, the effect of changes in CHT structure due to hydration is not considered in its performance. This study compares the effects on biocompatibility after drying at 25 °C and 150 °C scaffolds of chitosan, polyethylene glycol diglycidyl ether (PEGDE) crosslinked CHT (low, medium and high concentration) and glutaraldehyde (GA) crosslinked CHT. PEGDE crosslinked CHT showed a reduction in free amino groups and the amide I/II ratio, which exhaustive drying reduced further. In X-ray diffraction (DRX) analysis, PEGDE crosslinked CHT showed multiple peaks, whereas the crystallinity percentage was reduced with an increase in PEGDE concentration and thermal treatments at 150 °C. In a direct contact cell assay, high osteoblast viability was achieved at low and medium PEDGE concentrations, which was improved when the crosslinked scaffolds were thermally treated at 150 °C. This was attributed to its partial hydrophilicity, low crystallinity and low surface roughness; this in spite of the small reduction in the amount of free amino groups on the surface induced during drying at 150 °C. Furthermore, PEGDE crosslinked CHT scaffolds showed strong vinculin and integrin 1β expression, which render them suitable for bone contact applications.