Recently, nanoparticles (NPs) have drawn more interest because of their special qualities. In the agricultural and related sectors, metal-based NPs are frequently utilized. Examining the potential advantages and risks that different NPs may pose to microbial diversity and plants is the goal of this chapter. By directly influencing growth of the plant and indirectly the surroundings of ecological environment, nanoparticles can support the green revolution and ensure the sustainable growth of agriculture. Although the beneficial impacts of nanoparticles on the diversity of endophytic microbial communities in plants and around the rhizosphere have been well documented by several studies, some research continues to indicate that the effects of nanoparticles on microorganisms and plants may be dose dependent. The equilibrium of soil ecosystems may be upset by the overuse of nanoparticles. The process of interaction between nanoparticles and microbes must be thoroughly studied, and appropriate utilization techniques and dosages must be investigated, in order to maximize the advantages of nanoparticles and minimize any potential hazards. To guarantee the safe use of nanoparticles, it is also essential to improve the monitoring and assessment of potential environmental risks.