Plant diseases from pathogens and pests cause 20%–40% of global crop losses, threatening food security. Agrochemicals often control these issues but lead to pollution, resistance, and health risks. This chapter explores endophytic microorganisms as eco-friendly biocontrol agents. Endophytes produce metabolites that inhibit pathogens, induce systemic resistance, and enhance nutrient availability, offering a sustainable alternative for improving crop productivity and environmental health.