Scaffolds are three-dimensional porous structures that must have specific requirements to be applied in tissue engineering. Therefore, the study of factors affecting scaffold performance is of great importance. In this work, the optimal conditions for cross-linking preformed chitosan (CS) scaffolds by the tripolyphosphate polyanion (TPP) were investigated. The effect on scaffold physico-chemical properties of different concentrations of chitosan (1 and 2% w/v) and tripolyphosphate (1 and 2% w/v) as well as of cross-linking reaction times (2, 4, or 8 h) were studied. It was evidenced that a low CS concentration favored the formation of three-dimensional porous structures with a good pore interconnection while the use of more severe conditions in the cross-linking reaction (high TPP concentration and crosslinking reaction time) led to scaffolds with a suitable pore homogeneity, thermal stability, swelling behavior, and mechanical properties, but having a low pore interconnectivity. Preliminary biocompatibility tests showed a good osteoblasts’ viability when cultured on the scaffold obtained by CS 1%, TPP 1%, and an 8-h crosslinking time. These findings suggest how modulation of scaffold cross-linking conditions may permit to obtain chitosan scaffold with properly tuned morphological, mechanical and biological properties for application in the tissue regeneration field.