Nanotechnology involves synthesizing and applying diverse materials and devices by managing and controlling their shape and size at the nanoscale. In this sense, in the past two decades, the use of nanomaterials in the agriculture sector has been focused on the increment of crop yield by nanofertilizers, which can facilitate efficient nutrient uptake, soil fertility, water and nutrient absorption, increased photosynthesis, reduced soil toxicity, decreased application frequency, plant health improvement, and reduced environmental pollution. Nevertheless, some risks must be addressed before using these “smart tools” in food production. That is why one way to start on this path is the generation of green synthesis processes for nanofertilizers by using extracts from biological sources such as microorganisms and plants, obtaining more bio-compatible nanomaterials, boosting the advantages of its application and reducing the toxic effects over the environment.