Microbial biotoxins, produced by bacteria, fungi, and algae, have gained attention for their potential applications in biotechnology, especially in managing plant diseases and pests. These biotoxins have a range of bioactive properties, including antimicrobial, insecticidal, nematicidal, and herbicidal activities, making them promising candidates for sustainable and environmentally friendly solutions in agriculture. This review explores the diversity of microbial biotoxins and their mechanisms of action against plant pathogens and pests, as well as the biotechnological approaches used to harness these biotoxins for plant protection, including the development of biopesticides and genetically modified crops. The integration of microbial biotoxins into pest and disease management strategies has the potential to reduce reliance on chemical pesticides, minimize environmental impacts, and enhance crop yield and quality. The use of microbial biotoxins for pest control and their impact on agroecosystems has been documented. Biocontrol agents, such as predators and parasitoids, derived from bacteria, fungi, viruses, algae, protozoa, and entomopathogenic nematodes, are increasingly being used to develop microbial biopesticides as an alternative to chemical pesticides. As biotechnological advances continue to unravel their full potential, their role in sustainable agriculture is likely to expand, contributing to a more resilient and ecologically balanced food production system. The review highlights the diverse sources of microbial biotoxins, emphasizing their natural occurrence in the environment. Regulatory frameworks must ensure the safety of biotechnological products for both human health and the environment. Developing resistance in target pests and potential impacts on nontarget organisms must be carefully monitored and managed. Microbial biotoxins represent a valuable resource in the quest for sustainable and eco-friendly solutions to plant disease and pest management.