The geomorphological characteristics of the materials inherent in tropical soils, in addition to the excessive use of fertilizers and pesticides, industrial waste and residues, and novel pollutants derived from emerging new technologies such as nanomaterials, affect the functionality and resilience of the soil-microorganism-plant ecosystem; impacting phytoremediation processes and increasing the risk of heavy metal transfer into the food chain. The aim of this review is to provide a general overview of phytoremediation in tropical soils, placing special emphasis on the factors that affect this process, such as nanoagrochemicals, and highlighting the value of biodiversity among plant species that have the potential to grow and develop in soils impacted by heavy metals, as a useful resource upon which to base further research.