Biosynthesized nanoparticles (NPs) are emerging as promising tools in agriculture for enhancing crop productivity, nutrient uptake, and pest control. This chapter describes the interaction, toxicity, and fate of biosynthesized NPs within the agroecosystem. Various types of NPs, including metal, metal oxide, bimetallic, quantum dots, carbon-based, and organic NPs, are discussed, highlighting their unique compositions and characteristics. The complex interactions of NPs within the soil-plant system are explored, emphasizing their interactions with soil components, agricultural chemicals, and soil microbes. Factors influencing NP mobility and bioavailability, such as soil type, pH, and organic matter content, are examined. The chapter also addresses the uptake and translocation of NPs by plants and their impact on plant growth. The adsorption process within the soil matrix, which governs NP mobility and effectiveness, is thoroughly explained. As research continues, it is essential to understand these interactions thoroughly to balance the potential benefits and risks of using biosynthesized nanoparticles in agriculture, ensuring that soil health, crop productivity, and ecosystem functioning are maintained in the long term.