Nanotechnology has attracted remarkable attention due to its unique features and potential uses in multiple domains. Nanotechnology is a novel strategy to boost production from agriculture along with superior efficiency, ecological security, biological safety, and monetary security. Modern farming processes increasingly rely on environmentally sustainable techniques, providing substitutes for conventional fertilizers and pesticides. The drawbacks inherent in traditional agriculture can be addressed with the implementation of nanotechnology. Nanotechnology can uplift the global economy, so it becomes essential to explore the application of nanoparticles in agriculture. In-depth descriptions of the microbial synthesis of nanoparticles, the site and mode of action of nanoparticles in living cells and plants, the synthesis of nano-fertilizers and their effects on nutrient enhancement, the alleviation of abiotic stresses and plant diseases, and the interplay of nanoparticles with the metabolic processes of both plants and microbes are featured in this review. The antimicrobial activity, ROS-induced toxicity to cells, genetic damage, and growth promotion of plants are among the most often described mechanisms of operation of nanoparticles. The size, shape, and dosage of nanoparticles determine their ability to respond. Nevertheless, the mode of action of nano-enabled agri-chemicals has not been fully elucidated. The information provided in our review paper serves as an essential viewpoint when assessing the constraints and potential applications of employing nanomaterials in place of traditional fertilizers.