Metal-based nanoparticles (MNPs) are now widely used across industry, agriculture, and healthcare sectors thanks to their distinctive antimicrobial, catalytic, and physical-chemical characteristics. Nevertheless, their rising presence in land-based ecosystems—especially soil—has sparked concerns over potential environmental consequences. The most vulnerable targets are beneficial soil microorganisms, including bacteria and fungi, fundamental to nutrient cycling, organic matter decomposition, plant symbiosis, and overall soil health. This chapter comprehensively evaluates the ecotoxicological effects of MNPs on beneficial soil microbiota, emphasising the underlying mechanisms of toxicity, such as oxidative stress induction, membrane disruption, enzymatic inhibition, and genetic alterations. Special focus is given to key soil microbial groups that play pivotal roles in sustainable agriculture and ecosystem functioning. In addition to discussing the specific impacts of common MNPs such as AgNPs, CuNPs, ZnONPs, TiO₂NPs, and Fe₃O₄NPs, the chapter explores recent advances in mitigation strategies, including phytoremediation, bioremediation, and green nanoparticle synthesis. The role of regulatory frameworks and environmental risk assessment protocols is also examined, highlighting the need for more robust guidelines to ensure the safe integration of nanotechnologies into agricultural and environmental practices. Through this synthesis, the chapter contributes to a growing understanding of nanoparticle–microbe interactions and the need for environmentally conscious nanomaterial design.