Soil is a complex and dynamic ecosystem whose functionality is related to the equilibrium existing among chemical, physical and biological parameters and the resident microbial communities. Soil microorganisms play a central role in decomposing organic matter, in determining the release of mineral nutrients, and in nutrient cycling, and have direct and indirect effects on both crop growth and quality, as well as on the sustainability of soil productivity. In addition, soil microorganisms substantially contribute to the resistance and resilience of agro-ecosystems to abiotic disturbance and stress. Therefore, changes in microbial communities may directly affect soil ecosystem function since microbes can respond rapidly to environmental changes because of the vastness of microbial biomass and diversity. An increasing number of studies have shown how environmental impacts that cause modifications in microbial community structure and diversity ultimately affect soil biological processes. Agricultural land management is one of most significant anthropogenic activities that substantially alter soil characteristics, including physical, chemical, and biological properties. The present chapter gives a picture of the effect of different agricultural management practices on soil microbial community structure and function. A case study on the effects of tillage and nitrogen fertilization on soil bacterial community structure is also reported.