Packaging materials play an essential role in the preservation and marketing of food and other products. To improve their conservation capacity, antimicrobial agents that inhibit bacterial growth are used. Biopolymers such as starch and chitosan are a sustainable alternative for the generation of films for packaging that can also serve as a support for preservatives and antimicrobial agents. These substances can replace packaging of synthetic origin and maintain good functional properties to ensure the quality of food products. Films based on a mixture of corn starch and chitosan were developed by the casting method and the effect of incorporating cellulose nanocrystals (CNC) at different concentrations (0 to 10% w/w) was studied. The effect of the incorporation of CNC on the rheological, mechanical, thermal and barrier properties, as well as the antimicrobial activity of nanocomposite films, was evaluated. A significant modification of the functional and antimicrobial properties of the starch-chitosan films was observed with an increase in the concentration of nanomaterials. The films with CNC in a range of 0.5 to 5% presented the best performance. In line with the physicochemical characteristics which are desired in antimicrobial materials, this study can serve as a guide for the development this type of packaging for food use.