Nanomaterials are increasingly becoming important components of agricultural systems as fertilizers and pesticides with unmatched efficiency. The former has particularly revolutionized agriculture by offering targeted nutrient delivery and enhanced nutrient use efficiency. Additionally, nanofertilizers help in reducing environmental pollution by reducing the run-off of excess fertilizers and ensuring that nutrients are used effectively by crops. Despite their importance, the impacts of nanofertilizers on beneficial soilmicroorganisms, which are crucial components of agricultural systems and contributors to plant health and soil fertility, have remained the subject of considerable debate and investigation. This chapter probes the effects of nanofertilizers on rhizosphere microbial communities by exploring the effects on their populations, enzymes, and processes. The chapter examines the dynamic interplay between nanofertilizers and beneficial soilmicroorganisms and elucidates the alterations in microbial diversity, enzymes, and processes within the rhizosphere. Further, it delves into the mechanisms of nanofertilizer toxicity on beneficial soil microbes and the factors affecting the interactions between nanofertilizers and soil microbes to hypothesize the broader ecological implications and long-term sustainability. Therefore, the chapter sheds light on the intricate relationships between nanofertilizers and beneficial soilmicroorganisms and elucidates future strategies and research for sustainable and eco-friendly agricultural practices.