Phytoremediation is a green technology that aims to take up pollutants from soil or water. Metals are one of the targets of these techniques due to their high toxicity in biological systems, including plants and animals. Their elimination or, at least, decrease will help keep them from being incorporated in the trophic chain and thus reaching animal and human food. The metal removal efficiency of plants is closely related to their growth rate, tolerance, and their adaptability to different environments. Melatonin (N-acetyl-5-methoxytryptamine) is a ubiquitous molecule present in animals, plants, fungi, and bacteria. In plants, it plays an important role related to antioxidant activity, but also as an important redox network regulator. Thus, melatonin has been defined as a biostimulator of plant growth, especially under environmental stress conditions, whether abiotic (water deficit and waterlogging, extreme temperature, UV radiation, salinity, alkalinity, specific mineral deficit/excess, metals and other toxic compounds, etc.) or biotic (bacteria, fungi, and viruses). Exogenous melatonin treated plants have been seen to have a high tolerance to stressors, minimizing possible harmful effects through the control of reactive oxygen species (ROS) levels and activating antioxidative responses. Furthermore, important gene expression changes in stress specific transcription factors have been demonstrated. Melatonin is capable of mobilizing toxic metals, through phytochelatins, transporting this, while sequestration adds to the biostimulator effect of melatonin on plants, improving plant tolerance against toxic pollutants. Furthermore, melatonin improves the uptake of nitrogen (N), phosphorus (P), and sulfur (S) in stress situations, enhancing cell metabolism. In light of the above, the application of melatonin seems to be a useful option for clearing toxic pollutants from the environment by improving phytoremediation. Interestingly, a variety of stressors induce melatonin biosynthesis in plants, and the study of this endogenous response in hyperaccumulator plants may be even more interesting as a natural response of the phytoremediation of diverse plants.