The rapidly rising population is calling for the production of more food, yet biotic and abiotic stresses caused by pests and climate change substantially diminish crop yields. This issue may be partly solved by applying silica nanoparticles. Nanoparticles are small-sized particles ranging from 1 to 100 nm that possess enhanced physicochemical properties compared to the bulk material. For instance, the high surface-to-volume ratio of nanoparticles changes solubility, reactivity, and transportation speed in plants. Silica nanoparticles are now widely used in agriculture for the better growth of crops, with or without any stress. Silica nanoparticles can also be used as nano-fertilizers and nano-pesticides. Silica nanoparticles reduce biotic and abiotic stresses by enhancing the expression of anti-oxidant enzymes, osmoprotectants, proteins and secondary metabolites such as phenolic compounds. Silica nanoparticles also induce non-enzymatic defense responses by increasing the synthesis of ascorbic acid, proline, glutathione, and phytohormones. Here we review the use of silica nanoparticles in agriculture, with focus on synthesis, toxicity, mechanisms, uptake in plants, use as fertilizers and pesticides, and alleviation of biotic and abiotic stresses, such as pests, drought and toxic metals.