Microorganisms dominate virtually every environment on our planet, serving essential roles in various ecosystem functions. The ubiquity of microbes extends to the surfaces and internal environments of animals and plants. Within these eukaryotic hosts, microbes may modulate host physiology and their health. Given the metabolic potential of microbes and their importance in natural systems, the development of agricultural practices that promote microbial diversity and function may be essential for the long-term sustainability of arable land. In this chapter, the roles of microbial communities in agroecosystems, with emphasis on ecosystem function and resilience have been discussed. The methods for monitoring microbial community structure and function. Role of modern biotechnological tools in quantifying the microbial diversity and community composition have been discussed. The application and indiscriminate usage of fertilizers, pesticides, and other agriculture practices that may alter soil and plant microbial communities are described. Finally, the possibility of adopting practices that promote microbial diversity as well as direct application of microbial communities to soil to boost crop productivity are discussed.