Chitosan (CH) is a very well‐known biopolymer that has been widely used for the development of biomaterials with a wide range of applications in the biomedical field, such as the preparation of hydrogels, owing to its outstanding anti‐inflammatory, antibacterial and antifungal properties, biocompatibility and biodegradability, although they present limited mechanical properties. Chemical crosslinking is one of the most recurrent strategies for the reinforcement of these structures and, above all, crosslinking with natural‐origin compounds that do not compromise their biocompatibility is considered a hot topic in this research field. D‐fructose (F), obtained from the hydrolyzation and further isomerization of starch, an abundant raw material and genipin (G), which is extracted from the fruits of Gardenia jasminoides Ellis are used as natural crosslinkers. Chitosan‐based hydrogels crosslinked with each crosslinking agent are prepared and characterized through Fourier transform infrared (FTIR) spectroscopy, crosslinking and swelling degree determination, rheological, microstructural, and biological studies. The results demonstrate that crosslinking with G is more beneficial for chitosan‐based hydrogels since these samples showed more compact structures and better rheological performance. Additionally, excellent biological in vitro behavior due to the crosslinking with G, unlike that of F.