Selenium (Se) is a micronutrient in the environment that plays a vital role in microbial metabolism, where the inorganic and organic Se species get transformed and further dispersed in the soil-aqueous systems. Se has many beneficial aspects in managing stress response in plants to increase microbial diversity. Chemical and biological speciation of Se in the environment have many different routes where both oxidising and reducing microbes play a role in the availability of Se. bulk or nano Se can be used in conjugation with soil microbes to improve the soil quality, maintaining the threshold limit. This chapter describes the factors that can govern the interactions between arable soil microbiome and Se.