Soil is a dynamic, physically, spatially and temporally heterogeneous but well-organized, three-dimensional porous matrix mixing mineral and organic matter and living organisms. Among them, soil microbiota constitute a reservoir in which plants select a specific microbiome, contributing to their growth and their health. Microbes in soil also contribute to many ecosystemic services in agrosystems, as the recycling of major nutrients in the soil ecosystem (carbon, nitrogen, phosphorus, sulfur…). Nanoagrochemicals are active substances based on nanotechnologies and nanoformulations to improve the characteristics and properties of active molecules as pesticides for agronomy purposes, e.g., biocides, herbicides but also nutrients. Nanotechnologies have burst into agronomy with a potential for innovation in order to improve the efficiency of pesticides, nutrients, their delivery and thus contribute to the reduction of inputs in agriculture. However, the impact of these nanopesticides on the soil microbiota as non-target organism remains underestimated up to now. The chapter review the approaches and trends in the evaluation of nanopesticides implications on soil microbiota, focusing on copper-and silver-based nanoparticles as pesticides or on formulation or nanocarriers of conventional pesticides. By confronting the current knowledge and comparing methodologies, the potential and the pitfalls to overcome are discussed, together with future directions.