The effect of drying methods on chitosan reactivity towards Maillard reaction during storage of dried chitosan–lactose systems was investigated. Two different structural forms of chitosan, scaffold and microspheres, were prepared. Then they were dried by lyophilization or using supercritical fluid technology (SF-CO2) and stored with lactose under controlled temperature conditions (60 °C) and water activity (aw = 0.65). The drying method produced slight modifications on the chitosan structure especially in samples submitted to SF-CO2 treatment. Differences were more evident in the reactivity of chitosan–lactose systems during storage. Maillard reaction development was assessed by quantification of a new compound which originated from the acid hydrolysis of Amadori compounds (NFMD) resulting from chitosan–lactose interactions, and not detected in the acid hydrolysates of freshly prepared chitosan-lactose systems. Maillard reaction was influenced by different factors such as the manner of lactose addition, structure of chitosan (microspheres and scaffolds) and drying method. Lyophilized chitosan in the form of microspheres with lactose, presented the highest values of NFMD (428.45 mg/100 g of sample). The determination of this compound could be used as an index of the progress of Maillard reaction.