This work describes the synthesis and characterization of noncytotoxic nanocomposites either colloidal or as films exhibiting high antibacterial activity. The biocompatible and biodegradable polymer chitosan was used as reducing and stabilizing agent for the synthesis of gold nanoparticles embedded in it. Herein, for the first time, three different chitosan grades varying in the average molecular weight and deacetylation degree (DD) were used with an optimized gold precursor concentration. Several factors were analyzed in order to obtain antimicrobial but not cytotoxic nanocomposite materials. Films based on chitosan with medium molecular weight and the highest DD exhibited the highest antibacterial activity against biofilm forming strains of Staphylococcus aureus and Pseudomonas aeruginosa. The resulting nanocomposites did not show any cytotoxicity against mammalian somatic and tumoral cells. They produced a disruptive effect on the bacteria wall while their internalization was hindered on the eukaryotic cells. This selectivity and safety make them potentially applicable as antimicrobial coatings in the biomedical field.