<p>Nanoparticles (NPs) are emerging as transformative agro-intervention agents with significant potential for improving bioformulation delivery, pathogen control, and soil fertility management. However, their efficacy is governed by a dualistic, dose-dependent nature; while excessive concentrations may pose environmental risks, controlled low-level applications can stimulate beneficial microbial growth and enzymatic activities. This phenomenon, known as hormesis, is essential for optimizing the nutrient cycling necessary for sustainable soil health. This review synthesizes contemporary insights into the varied impacts of NPs on agriculturally beneficial microbial (ABM) systems, particularly focusing on biological nitrogen fixation (BNF), interactions with arbuscular mycorrhizal fungi (AMF), and the production of secondary metabolites such as siderophores and volatile organic compounds (VOCs). The review explicates mechanisms of NP-induced enzyme activity, relating these to the complexities of real soil environments, including factors like pH, organic matter content, and mineralogy, which influence NP behavior and bioavailability. Furthermore, it explores enzymatic activation pathways and proposes a framework for NP-microbe signaling involving reactive oxygen species (ROS) and microbial gene expression modulation. The authors stress the need for environmentally mindful NP designs, standardized ecological assessments via life cycle assessments (LCA), and robust regulations for the safe incorporation of nanotechnology in agriculture, which is necessary for fostering healthy soils and sustainable plant growth. Additionally, it highlights cutting-edge research on NP-mediated CRISPR-Cas technology for targeted microbial modifications and the role of deep neural networks (DNNs) in nano-ecotoxicology predictions, thereby linking nanoscience with microbial ecology to inform future research and agricultural policy. This review provides a holistic perspective that bridges nanoscience and microbial ecology, paving the way for sustainable innovation in managing soil health and plant nutrition.</p> Graphical abstract <p>Engineered nanoparticles influence the soil–plant–microbiome system. The figure summarizes beneficial effects such as improved nutrient cycling, plant growth promotion, nitrogen fixation support, pathogen suppression, and quorum sensing disruption, alongside potential risks including microbial resistance development and enhanced horizontal transfer of antibiotic resistance genes under prolonged or high-dose nanoparticle exposure. Abbreviations: NP= Nanoparticle; NPs = Nanoparticles; AMF = Arbuscular mycorrhizal fungi; RAM: Rhizospheric beneficial microorganisms; nHAP= Nano hydroxyapatite; HGT = Horizontal gene transfer; ARGs = Antibiotic resistance genes; Low and high dose effects indicate concentration-dependent biological responses in agroecosystems</p> <p></p>