Selenium (Se) plays crucial roles in human, animal, and plant physiology, but its varied plant functions remain complex and not fully understood. While Se deficiency affects over a billion people worldwide, excessive Se levels can be toxic, presenting substantial risks to ecosystem health and public safety. The delicate balance between Se's beneficial and harmful effects necessitates a deeper understanding of its speciation dynamics and how different organisms within ecosystems respond to Se. Since humans primarily consume Se through Se-rich foods, exploring Se's behavior, uptake, and transport within agroecosystems is critical to creating effective management strategies. Traditional physicochemical methods for Se remediation are often expensive and potentially harmful to the environment, pushing the need for more sustainable solutions. In recent years, phytotechnologies have gained traction as a promising approach to Se management by harnessing plants' natural abilities to absorb, accumulate, metabolize, and volatilize Se. These strategies range from boosting Se uptake and tolerance in plants to releasing Se as less toxic volatile compounds or utilizing it as a biofortified supplement, opening up diverse possibilities for managing Se, offering sustainable pathways to improve crop nutritional quality, and protecting human health in different environmental contexts. However, closing the gaps in our understanding of Se dynamics within agricultural systems calls for a united front of interdisciplinary collaboration from biology to environmental science, agriculture, and public health, which has a crucial role to play. Phytotechnologies offer a sustainable bridge between Se deficiency and toxicity, but further research is needed to optimize these methods and explore their potential in various agricultural and environmental settings. By shedding light on Se's multifaceted roles and refining management strategies, this review contributes to developing cost-effective and eco-friendly approaches for Se management in agroecosystems. It aims to lead the way toward a healthier and more sustainable future by balancing the need to address Se deficiency and mitigate the risks of Se toxicity.