Gastrointestinal disorders, such as irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD, including Chron’s disease and ulcerative colitis), affect 10–15% of the global population resulting in a substantial socioeconomic burden on our society.1 Mucosal biofilms are mucus-adherent prokaryotic communities embedded in a protective layer of extracellular substances, displaying high antibiotic resistance,2 and occur in 57% of IBS patients and 34% of ulcerative colitis patients.3 Antimicrobial peptides (AMPs) of natural origin evolved for their activity to combat bacteria,4 representing therapeutic opportunities for treating infectious diseases. However, the full potential of such AMPs against gut mucosal biofilms has not been revealed yet. Our approach focuses on developing gut biofilm-targeting peptides, including (i) synthesis of AMPs from diverse natural sources, (ii) screening for biofilm-specific activity against bacterial isolates from biofilm-positive patients, and (iii) chemical strategies to improve our AMP leads’ gut stability and therapeutic window. Here, we report our latest results in developing gut-specific antibiofilm peptides to treat mucosal biofilms in patients with gastrointestinal disorders.