Microbial biodiversity is an integral part of a natural environment that delivers essential services for the proper functioning of agroecosystems and associated flora and fauna. Hence, continuous exploration of microbial biodiversity, function, resilience and biodiversity conservation while addressing threats to microbial diversity in agricultural settings becomes mandatory. This chapter highlights the multifaceted roles of microbes in agroecosystems, including nutrient cycling, plant-microbe interactions, and biocontrol of plant diseases. Discussions related to symbiotic relationships such as mycorrhizal associations and rhizobia-legume symbiosis, as well as the role of plant growth-promoting rhizobacteria (PGPR) and microbial-induced systemic resistance (ISR) in plant health are included. The chapter also investigates the link between microbial diversity and climate change resilience, including microbial contributions to carbon sequestration and greenhouse gas mitigation. Challenges to microbial biodiversity in agroecosystems, such as land-use changes and environmental contamination are also addressed here. Strategies for preserving microbial biodiversity are proposed, including cataloguing initiatives and incorporating microbial diversity into agricultural management. The chapter concludes by emphasizing the potential of harnessing microbial contributions for sustainable agriculture and ecosystem resilience, highlighting the need for further research in microbial ecology and agroecosystem management.