Currently, an emerging bionanomaterial in sustainable agriculture is the microbial nanoparticle (NP), providing green alternatives to overcome chemical fertilizers and pesticides. The ecofriendly microbial nanofactories possess NPs with distinct physiochemical traits supporting the manifold agriculturalAgricultural yields. Microbes as bacteriaBacteria, fungiFungi, algae, and viruses act as biofertilizers increasing the nutrientNutrient uptake by plants by improvising solubility with controlled release, thus enhancing the crop yield with reduced stress. These beneficial rhizosphere microbes deliver the metabolites to strengthen the soil fertility along with the plant-microbial interactions. Due to their greater bioactivities and surface area, these microbial NPs align with precise farming techniques to help minimize water and soil contaminations. Likewise, microbial NPs also assist as biocontrol agents, displaying robust antimicrobial and pesticidal effects with various mechanisms like disrupting membrane, metabolic pathways disruption, and reactive oxygen species generation. Following controlled metabolite release by NPs ensures long-lasting crop protection with lesser ecological risk. The following chapter reviews the synthesis strategies, functional mechanisms, and ecological advantages of microbial NPs while also considering challenges with scalability, regulation, and environmental safety. By combining nanotechnology with microbiology, microbial NPs offer a sustainable route to boost productivity, reduce chemical reliance, and promote agro-ecological balance.