Strategies aimed at defining, discovering, and developing alternatives to traditional antibiotics will underlie the development of sustainable agricultural systems. Among such strategies, antimicrobial peptides (AMPs) with broad-spectrum antimicrobial activity and multifaceted mechanisms of action are recognized as ideal alternatives in the post-antibiotic era. In particular, AMPs derived from microbes with active metabolisms that can adapt to a variety of extreme environments have long been sought after. Consequently, this review summarizes information on naturally occurring AMPs, including their biological activity, antimicrobial mechanisms, and the preparation of microbial-derived AMPs; it also outlines their applications and the challenges presented by their use in the agroindustry. By dissecting the research results on microbial-derived AMPs of previous generations, this study contributes valuable knowledge on the exploration and realization of the applications of AMPs in sustainable agriculture.