Nanotechnology is a current field that is presenting unprecedented possibilities to improve soil fertility and health. Based on the success, several late-generation nanomaterials used as fertilizers and plant biostimulant products have been used extensively in several agricultural regions worldwide, generating serious concerns regarding biosafety for the environment and consumers of agricultural products. This chapter aimed to show a general landscape about some examples regarding the problematic abovementioned of using nanomaterials in agriculture, with emphasis on aspects related to soil fertility and health involved in plant production, as well as the microbiome associated with these ecosystems. The latter obviously creates concern in people regarding possible future problems of this technology used in agriculture.