The dye adsorption by chitosan is considered an alternative and eco-friendly technology, however, when chitosan structure is chemically modified it can result in a more suitable adsorbent. In this work, cyanoguanidine-crosslinked chitosan (CC-chitosan) was prepared and characterized, and it was applied for the adsorption of Food Blue 2 and Food Yellow 4 in the aqueous binary system. The equilibrium curves showed adequate to fit the extended Langmuir model at different temperatures. The equilibrium results showed that the more suitable conditions for the food dye adsorption in a binary system were at 288K, and the maximum adsorption capacities were around 595–680mgg−1. Avrami model was the most appropriate to fit the kinetic behavior, and desorption was possible for two cycles. On the basis of FT-IR spectrums, it was shown that cyanoguanidine was successfully inserted on the chitosan polymeric chains. CC-chitosan was an efficient adsorbent in removing dyes from aqueous binary systems.