In recent years, active packaging has been introduced as a new method to better preserve food. Chitosan and nanoclay have been used for preparation of an active nanocomposite with respect to their antimicrobial properties to investigate its effects on the microbial limitation in Gouda cheese. Nanoclay film, chitosan film, chitosan-based nanocomposites and nanoclay-based nanocomposites were prepared and their antimicrobial properties were evaluated to the microbial limitations of Gouda cheese consist of coliforms, Escherichia coli, Salmonella spp., coagulase-positive Staphylococcus, mold and yeast by agar diffusion method. The results indicated, the best antimicrobial effect belonged to nanocomposite film with the composition of chitosan 3 wt% by adding nanoclay 1 wt%, which can prevent microbial characteristics of Gouda cheese. The chitosan and nanoclay nanocomposite had excellent antibacterial activity and performed well against microbial limitations (coliforms, E. coli, Salmonella spp., coagulase-positive Staphylococcus, mold and yeast) of Gouda cheese. Therefore, the nanocomposite may be possibly used as a surface coating in addition to Gouda cheese as well as similar cheeses and other food to enhance microbial characteristics and extend shelf life.