Selenium (Se) is an essential trace element of fundamental importance to humans, animals and plants. However, the uptake, transport and metabolic processes of Se and their underlying mechanisms in plants have not been well characterized. Here, we review our current understanding of the adsorption and assimilation of Se in plants. First, we discussed the conversion of Se from inorganic Se into organic forms, the mechanisms underlying the formation of seleno-amino acids and the detoxification of Se. We then discussed the ways in which Se protects plants against toxic metal ions in the environment, such as by alleviating oxidative stress, regulating the activity of antioxidant enzymes, sequestering metal ions and preventing metal ion uptake and accumulation. Generally, this review will aid future research examining the molecular mechanisms underlying the antagonistic relationships between Se and toxic metals in plants.© The Author(s) 2021. Published by Oxford University Press on behalf of Royal Society of Chemistry.