The antibacterial activity of N,O-acylated chitosan derivative with linoleic acid (CH_LA) was tested by disc and well diffusion, agar impregnation and microdilution methods against Staphylococcus aureus, Escherichia coli and Helicobacter pylori strains. Hydrophobically modified chitosan (HMC) was expected to exhibit enhanced antibacterial activity and specific mucin interactions. Although diffusion tests have not indicated the antibacterial potential of chitosan (CH) or CH_LA, the results of the microdilution method demonstrated that tested polymers significantly reduced the amount of living bacteria cells in different concentrations depending on the microorganism. Additionally, CH_LA was characterized by enhanced antibacterial activity compared to CH, which may suggest a different mechanism of interaction with S. aureus and H. pylori. Furthermore, the UV-VIS analysis revealed that the amphiphilic character of derivative led to strong CH_LA–mucin interactions. The study proved the high potential of CH_LA in antibacterial applications, especially for the gastrointestinal tract.