A staggering number of nanomaterials-based products are being engineered and produced commercially. Many of these engineered nanomaterials (ENMs) are finally disposed into the soil through various routes in enormous quantities. Nanomaterials are also being specially tailored for their use in agriculture as nano-fertilizers, nano-pesticides, and nano-based biosensors, which is leading to their accumulation in the soil. The presence of ENMs considerably affects the soil microbiome, including the abundance and diversity of microbes. In addition, they also influence crucial microbial processes, such as nitrogen fixation, mineralization, and plant growth promoting activities. ENMs conduct in soil is typically dependent on various properties of ENMs and soil. Among nanoparticles, silver and zinc oxide have been extensively prepared and studied owing to their excellent industrial properties and well-known antimicrobial activities. Therefore, at this stage, it is imperative to understand how these ENMs influence the soil microbiome and related processes. These investigations will provide necessary information to regulate the applications of ENMs for sustainable agriculture and may help in increasing agrarian production. Therefore, this review discusses several such issues.