Nanotechnology is a key player in the agro-technological revolution, offering the potential to reform the agricultural system and improve food security, as conventional farming methods often cause crop damage due to pest infestations and natural disasters. Nanotechnology provides potential solutions to increase agricultural productivity and overcome the limitations of the “Green Revolution.” Researchers have conducted extensive research on the use of nanoparticles in agriculture. Nano-agrochemicals, such as nano-pesticides and nano-fertilizers, introduce nanomaterials, including nanoparticles and nano-formulations, into agro-ecosystems. Researchers have studied the potentially toxic effects of nanomaterials on environmental and biological systems, including soil microbiota, which have led to infertility and varying responses from soil fungi and bacteria. Nanometer-scale materials have unique physicochemical properties, leading to increased research and an established economic venture due to their potential usage. Despite their gifted nature, many studies have shown the potentially toxic effects that nanomaterials can have on environmental and biological systems. Therefore, the scientific community has focused its attention on studying the detrimental effects of nanomaterials. As a result, literature compiled in a laboratory or on a larger scale focuses on the physiological, biochemical, molecular, and genotoxic effects of nanomaterials. The chapter discusses the toxic effects of nanomaterials on agro-ecosystems and food chains, offering insights for safer and more sustainable use.