Engineered nanomaterials (ENMs) have huge potential for improving use efficiency of agrochemicals, crop production, and soil health; however, the behavior and fate of ENMs and the potential for negative long‐term impacts to agroecosystems remain largely unknown. In particular, there is a lack of clear understanding of the transformation of ENMs in both soil and plant compartments. The transformation can be physical, chemical, and/or biological, and may occur in soil, at the plant interface, and/or inside the plant. Due to these highly dynamic processes, ENMs may acquire new properties distinct from their original profile; as such, the behavior, fate, and biological effects may also differ significantly. Several essential questions in terms of ENMs transformation are discussed, including the drivers and locations of ENM transformation in the soil–plant system and the effects of ENM transformation on analyte uptake, translocation, and toxicity. The main knowledge gaps in this area are highlighted and future research needs are outlined so as to ensure sustainable nanoenabled agricultural applications. Transformation of engineered nanomaterials (ENMs) determines their environmental fate and impacts. Several essential questions including the drivers and locations of ENM transformation in the soil–plant system and the effects of ENMs transformation on their uptake, translocation, and toxicity are discussed. The main knowledge gaps in this area are highlighted and future research needs are outlined so as to ensure sustainable nanoenabled agricultural applications.