Biocontrol, or protection, involves using living organisms such as microbes, insects, and their by-products to safeguard food security against harmful pathogens and pests in agriculture. Excessive use of synthetic inputs such as fertilizers and pesticides in farming can lead to soil accumulation and crust formation over time. Inorganic chemical pollutants enter the food chain through plant absorption from the soil, resulting in environmental and public health concerns. Compensating for the destructive effects of synthetic pesticides on agroecosystems is challenging. Therefore, it is important to discuss the future of plant health and the restoration of microbial communities in the phyllosphere, endosphere, rhizosphere, and plant growth–promoting microorganisms using natural sources. Local governments should enforce legal restrictions on the frequency and quantity of conventional pesticide use, promote the use of bioagents, and encourage farmers and stakeholders to adopt natural alternatives. This chapter introduces various bio-based materials that can serve as natural alternatives to synthetic chemicals for eradicating or minimizing invasive phytopathogen species through biocontrol in plant protection.