Nanoparticles (NPs) have biological activity against microorganisms and plants, though they also have an aggregating tendency. Consequently, NPs serve as an important source of soluble metals, thereby exposing organisms to toxicities that are specific to both ions and particles. This chapter delves into the synthesis and modification processes of nanoparticles (NPs), shedding light on how various synthesis methods and surface alterations can influence NP properties and their interactions with plants and soil bacteria. It examines the substantial influence of NPs on crucial biological processes vital for soil fertility and plant yield, whether they are deliberately or accidentally introduced. Despite these challenges, the coordination among soil pore water, plant root exudates, and microbial cell surfaces serves to diminish NP bioactivity. Interestingly, the interactions of NPs with microbial cells and plants offer unexpected opportunities for extracting commercially valuable metabolites. Furthermore, the chapter delves into the potential utilization of engineered nanomaterials (ENMs) to enhance plant health and nutrient availability, thereby boosting plant productivity. Engineered nanomaterials (ENMs) find wide-ranging applications in many aspects of the plant system, such as quality improvement, growth promotion, and genetic preservation. However, it’s crucial to note that their impact may also include adverse effects on plant physiology and growth suppression, emphasizing the importance of a comprehensive understanding of NP-plant interactions. Overall, this chapter clarifies the complex effects of NPs on soil ecosystems and plant health by summarizing the most recent research findings.