Currently, metal nanoparticles have varied uses for different medical, pharmaceutical, and agricultural applications. Nanobiotechnology, combined with green chemistry, has great potential for the development of novel and necessary products that benefit human health, environment, and industries. Green chemistry has an important role due to its contribution to unconventional synthesis methods of gold and silver nanoparticles from plant extracts, which have exhibited antimicrobial potential, among other outstanding properties. Biodiversity-rich countries need to collect and convert knowledge from biological resources into processes, compounds, methods, and tools, which need to be achieved along with sustainable use and exploitation of biological diversity. Therefore, this paper describes the relevant reported green synthesis of gold and silver nanoparticles from plant extracts and their capacity as antimicrobial agents within the agricultural field for fighting against bacterial and fungal pathogens that can cause plant, waterborne, and foodborne diseases. Moreover, this work makes a brief review of nanoparticles’ contribution to water treatment and the development of “environmentally-friendly” nanofertilizers, nanopesticides, and nanoherbicides, as well as presenting the harmful effects of nanoparticles accumulation in plants and soils.