The ever-increasing population and the depletion of land and other resources provide the agriculture sector with enormous hurdles in satisfying the expanding demand for food. In an attempt to overcome these challenges, some essential inputs, such as fertilizers, pesticides, and other agrochemicals, are abused, resulting in environmental damage. Neglecting ecological sustainability and favoring massive agricultural production has led to declining soil health, degraded land, and severe ecological problems. Increasing agricultural output under sustainable conditions should be the main goal of future efforts to feed the expanding population. In modern agriculture, one major concern is that agricultural pests are evolving resistance to pesticides. Future crop production must be assured by applying innovative strategies that increase crop yields while preserving the environment. Among all the biota in soil, soil microbes are the most prevalent and are responsible for various aspects of ecosystem functioning, such as soil fertility, plant health, primary production, controlling plant pests, and bioremediation of both organic and inorganic. A considerable number of these organisms are naturally found in the soil, but in certain circumstances, it could be advantageous to boost their numbers by inoculation or the use of certain agricultural management strategies that improve their activity and abundance. This chapter provides a comprehensive overview of the mechanisms of soil microorganisms involved in pests’ biocontrol and polluted soil remediation. Furthermore, the advantages and disadvantages of the microbial rhizosphere for agricultural sustainability are discussed.