In recent years, the scientific community has shown significant interest in bioactive peptides as potential therapeutic agents. Bioactive peptides are short peptide chains that offer several health benefits, such as antimicrobial, antihypertensive, and anticancer properties that can be used for prevention and treatment of a variety of diseases. Food, a major source of bioactive peptides, can be used to produce bioactive peptides through either enzymatic hydrolysis or fermentation with starting cultures. Resistance of microbes to available antibiotics has become a grave concern and has necessitated the search for alternative treatment strategies in addition to small-molecule antibiotics. Food-derived bioactive peptides can act as natural antimicrobial agents, as they can inhibit the growth and activity of various pathogenic microbes, such as bacteria, fungi, and viruses. These bioactive peptides with antimicrobial properties can be investigated as novel and effective therapeutics agents, with the goal of addressing the growing burden of antimicrobial resistance. This chapter provides a comprehensive review of the bioactive peptides as potential antimicrobial agents and examines the challenges and opportunities in this area of research.