Selenium (Se), as an essential micro-nutrient that enhances plant growth by boosting photosynthesis and is playing a key role in stress tolerance against abiotic stresses activating antioxidant systems in plants. The Se availability in soil is ranging from 0.01 to 2.0 mg/kg with the average of 0.4 mg/kg and 10–25% of <0.4 mg per kg can be directly uptake by plants. The Se uptake by plants depends on interactions among soil properties, microbe species and their activities, plant species and growth stage. There are four inorganic Se species found in soil; Selenate ( \({\text{SeO}}_{4}^{2 - }\) ) and Selenite ( \({\text{SeO}}_{3}^{2 - }\) ) are highly soluble and readily absorb by plants. The organic Se fractions include seleno-methionine (SeMet), seleno-cysteine (SeCys), and methyl-selenocysteine. As a redox active element, the bioavailability of Se relies of valent status that determines by microbe driven chemical transformations by oxidoreductions and methylation-demethylation. The seleno-bacteria and arbuscular mycorrhizal fungi (AMF) are the two microbial groups significantly enhance Se bioavailability by metabolic conversions. The seleno-bacterial species of Pseudomonas, Stenotrophomonas, Bacillus, Providencia, Proteus are found to be particularly efficient in Se bioavailability while species of Rhizophagus, Funneliformis and Glomus are the reliable AM fungi reported so far. In addition, many other fungal species have significant contributions in Se behavior in soil–plant-atmosphere system. The net absorption of Se in plants depends of bioavailability of the element, adsorption/desorption properties of soil, redox potential and plant specific characteristics. In this chapter, we focus on the bio-geochemical transformations of Se, particularly the interaction between soil properties and microbial processes that determine Se bioavailability as well as the plant uptake of Se. This highlights the unique role of microbes in Se biofortification and stresses the need for novel approaches in sustainable agricultural practices in the context of drought, salinity, heavy metal pollution, and temperature extremes.