Farmers have relied on synthetic agrochemicals at various stages of crop production to meet the increasing demand for food yield. However, the overuse of these products has led to the contamination and degradation of ecosystems, water, and soils. In addition, climate change and resource scarcity are part of the growing threat that compromises food security for future generations. New agricultural trends focus on organic and sustainable practices where plant protection is achieved and yields are met by applying microbial and plant extracts containing bioactive substances that function as biofertilizers, biopesticides, and biostimulants. Although these products yield positive results, they lose activity and effectiveness once applied due to their sensitivity to environmental factors. Efforts to improve these products with nanobiotechnology through their encapsulation in different biopolymeric networks offer an eco-friendly and viable alternative that provides stability, bioavailability, and a controlled release of these compounds with the sole intention of ensuring crop protection, plant development, and product quality against diverse biotic and abiotic factors while making an efficient use of resources. Thus, this chapter highlights and emphasizes the use of biomaterials for the nanoencapsulation of bioactive substances to enhance their effect on plant growth and protection against environmental factors, weeds, insects, and diseases.