The advancement of agriusable nanocompounds has revealed their significant potential in enhancing crop performance. Nanomaterials (NMs), particularly those with dimensions ranging from 1 to 100 nm, whether metal-based or organic, not only impact crop growth but also influence the soil ecosystem upon application. These materials can modify the functional properties of soil, which serves as a habitat for a diverse range of microorganisms responsible for critical processes such as soil formation, nutrient cycling, and plant growth promotion. Understanding the effects of NMs on soil microbial communities, enzymatic activities, and nutrient dynamics is essential for optimizing their application. While some studies highlight the beneficial impacts of NMs on soil health, others indicate adverse effects on microbial populations. Consequently, the careful selection of NMs is vital to maximize their efficacy while safeguarding the integrity of the soil ecosystem. Moreover, the integration of machine learning tools presents a novel approach to predicting the impacts of NMs on soil functions, enhancing our ability to assess and manage these interactions effectively. This chapter comprehensively illuminates the diverse effects of NMs on soil microbiota and functions, contributing to an understanding of their environmental significance and implications for sustainable agricultural practices.