Climate change threatens crop yields and food security, particularly through heat stress and water scarcity, with projected declines in the productivity of key crops. Additionally, climate-induced nutrient deficiencies impact human health, contributing to oxidative stress-related diseases, and urges for sustainable agricultural practices. Selenium (Se) is an essential element that benefits not only animals and humans but also plants. In some regions globally, dietary Se deficiency is a prevalent issue. To address this concern, Se compounds have been applied to enhance the Se levels in the edible portions of crops, either through foliar sprays or by incorporating them into fertilizers. Also, Se has demonstrated the ability to mitigate various abiotic stresses in plants such as cold, drought, high light, salinity, and heavy metals, although the underlying mechanisms are complex and not yet fully understood. Many studies have suggested that Se is involved in several mechanisms: regulating reactive oxygen species (ROS) and antioxidants, inhibiting the uptake and movement of heavy metals, and improving the uptake of other essential nutrients. Moreover, Se can influence the regulation of the uptake and redistribution of elements that are vital for antioxidative systems or for maintaining ionic balance and structural integrity in cells. Also, Se can potentially disrupt electron transport by influencing the assembly of the complexes related to photosynthesis. As a consequence, the biofortification of fundamental food crops like cereals, legumes, vegetables, fruits, and medicinal plants by Se supplementation has been currently in trend. However, both low and high Se intake can significantly impact animal and plant health, making Se a ‘double-edged sword’. Therefore, future studies should increasingly investigate the dynamics of cellular distribution and accumulation during abiotic stresses and the other possible mechanisms involved in Se-mediated stress tolerance.