Plant growth-promoting rhizobacteria (PGPR) are beneficial soil bacteria that may influence plant development directly and indirectly. These organisms may be capable of limiting or replacing the need for synthetic fertilizers and harmful chemical inputs. Therefore, investigating the use of PGPR in agriculture is considered a promising method for enhancing agricultural productivity while minimizing negative impacts on ecosystems. The utilization of nanotechnology in agriculture is also growing extensively, resulting in the presence of a significant quantity of engineered nanomaterials (ENMs) in soil. Therefore, the use of ENMs has the potential to bring about groundbreaking changes in the agricultural industry. Great potential exists for using PGPR in the application of ENMs such as silica, gold, titanium, zinc oxide, and silver. The use of PGPR in conjunction with ENMs may prove to be advantageous in terms of successfully managing plant development and increasing productivity. Key microbial processes may be impacted by the presence and persistence of these ENMs in the soil, which can change the soil microbiome’s quality. Nevertheless, it is conceivable that ENMs can exert both beneficial and detrimental effects on certain PGPR species. This chapter evaluates ENMs to explore their potential as eco-friendly agents for application in the field. The primary emphasis will be on ENMs, which are expected to accumulate at the highest levels in terrestrial ecosystems. It also seeks to understand how ENMs affect soil microbiota and review what is known about the toxicity of ENMs to important soil microorganisms. This chapter provides the data required for future regulations on the proper use of ENMs for more productive and sustainable agriculture. Furthermore, future studies should focus on a full examination of nanotoxicity in bacterial ecosystems, particularly on chemicals that stimulate plant development.