Chitosan, a natural polymer derived from chitin by deacetylation process of chitin, has gained an enormous interest in tissue engineering due to its unique features such as antibacterial activity and wound healing properties. Electrospinning of acidified chitosan solution is one of the most widely-used approaches in fabrication of 3D scaffolds. Although there are some reports addressing morphology tailoring of the chitosan nanofibers through solution electrospinning, there is no comparative report concerning the neutralization and stabilization conditions of chitosan electrospun fibers. Therefore, this article compares the effects of different neutralizing agents such as aqueous solutions of sodium carbonate (Na2CO3) and potassium carbonate (K2CO3), and crosslinking reagents including glutaraldehyde (GA) and genipin on morphology of electrospun chitosan fibers. After neutralization and stabilization processes, Fourier transform infrared spectroscopy (FTIR) was employed to investigate the morphology of fibers. Furthermore, the influence of the aforementioned parameters on stability of fibers was probed using scanning electron microscopy. SEM images illustrated that the scaffold resulting from electrospinning of 4 wt% chitosan solution in a mixture of trifluoroacetic acid (TFA) and dichloromethane (DCM) possessed a well-formed nanofibrous structure. Afterwards, different methods for neutralization and stabilization of the electrospun chitosan nanofiber mats were performed. In this respect, aqueous solutions of both Na2CO3 and K2CO3 salts (1M) were employed as neutralization agents and GA and genipin were used as two different crosslinking agents. Based on SEM analysis, the chitosan fibers, crosslinked with genipin, showed better morphology than a scaffold which was crosslinked with glutaraldehyd