Soil is a dynamic and complex biological system. Mineral mining, continuous cropping, soil erosion and unsuitable land-use practices have mostly caused the loss of fertile soil. Because these soils are intensively used for crop production, their productivity and functionality are severely impaired. Soil degradation is a continuous process, and the consequences of climate change exacerbate it. Climate change and environmental pressures are particularly harmful to soils and crops. Soil microbial diversity and ecosystem services offered by soils are under threat in many agro-ecosystems due to various natural and human factors. The loss of biodiversityBiodiversity has become a worldwide issue as evidence mounts that it will negatively impact ecosystem services. Modern agronomic methods that disrupt soil trophic networks and reduce long-term soil productivity are common in agricultural soils. The use of toxic agrochemicals, mono-cropping, extensive tillage, and other agricultural management practices affects soil microbial community structure and soil sustainability. As a result, changes occur in the soil microbial community structure, affecting the physical, chemical, and biological characteristics of the soil. In this chapter, we discuss the importance of soil microbial diversity and its role in soil quality and fertility, the contribution of soil microbes to soil structure, nutrient acquisition and circulation, and pollutant degradation.