Due to the widespread use of engineered nanomaterials (ENMs) for soil remediation and nano-enabled sustainable agriculture, there is a growing concern regarding the behavior and fate of ENMs released into soil systems in the presence of natural root exudates (REs). Herein, we investigate the influence of REs on the fate and ecological effect of ENMs from a comprehensive perspective. We summarize the key roles reported in the literature for REs in physical changes (e.g., adsorption, dispersion/aggregation), chemical changes (e.g., oxidation/redox reactions, and dissolution), and biotransformation of ENMs, which will further determine the ecological risk of ENMs in natural soil systems. Moreover, this review highlights the potential adverse effects of ENMs on different soil organisms (e.g., bacteria, plants, and eisenia foetida) in the presence of REs. The remaining unclear mechanisms (e.g., oxidative stress and DNA damage) of ENMs toxicity at the cellular level influenced by REs are reviewed and presented. Finally, the review concludes by addressing the current knowledge gaps and challenges in this field.