Nanotechnology proved as a boon to this era and is widely applied in many areas of science and technology. Agriculture is the backbone of industrial raw material and it is very important to have technologies supporting high yield, better crop production and protection in a cost effective, ecofriendly and sustainable way. Globally, there is a lot of research being conducted in the field of application of nanoparticles in agriculture. In recent time nano-based materials like nanoparticles and nanoformulations, nano-based fertilizers, nano-pesticides and insecticides, nano fungicides and other plant disease control formulations are available in the market. Though this technology offers many advantages, yet there are some vices which is causing the concern among the researchers and practitioners. The unregulated exposure of the nanoparticles to the soil is expected to cause adverse effects on the soil microbiota and in some cases negatively impact the important adaphic factors like soil infertility and toxicity. The studies conducted so far have shown diverse responses of nanoparticles by soil fungi and soil bacteria. The enzymatic activities of the microbes have been reported to be affected when the stress is induced from different sources. In some studies, silver nanoparticles have been found to decrease FDA-hydrolysis in soil. More research still needs to be done on addressing the nanoparticle induced metal-stress by different microbes. This review provides the comprehensive account of side effects of the nanoparticles on soil fertility and their effect on the different properties of soil and plant growth along with the research gaps in the field of soil application of nanoparticles and way forward to introduce an ecofriendly application of nanoparticles.