Phytoremediation is an eco-friendly technology that utilizes plants and plant–microbe interactions to remove a wide spectrum of organic and inorganic pollutants from contaminated environments such as soils, waters and sediments. This low-impact, environmentally sustainable and cost-effective methodology represents a valuable alternative to expensive physical and chemical approaches, characterized by secondary pollution risks, and is gaining increasing attention from researchers and popular acceptance. In this review, the main mechanisms underlying the decontamination activity of plants have been clarified, highlighting the environmental remediation in fertility and soil health. Studies have illustrated the high potential of phytoremediation coupled with green and sustainable biocatalytic processes, which together represent a non-polluting alternative for the conversion of plant biomass into renewable resources. The convenience of this technology also lies in the valorization of the bio-wastes towards biofuels, energy purposes and value-added products, contributing to an effective and sustainable circular approach to phyto-management. The strategy proposed in this work allows, with the use of totally green technologies, the recovery and valorization of contaminated soil and, at the same time, the production of bioenergy with high efficiency, within the framework of international programs for the development of the circular economy and the reduction of greenhouse carbon emissions.