A screening-level analysis that considers system-wide benefits and costs is used to identify opportunities where engineered nanomaterials can advance the sustainability of crop-based agriculture. The globally recognized need to advance more sustainable agriculture and food systems has motivated the emergence of transdisciplinary solutions, which include methodologies that utilize the properties of materials at the nanoscale to address extensive and inefficient resource use. Despite the promising prospects of these nanoscale materials, the potential for large-scale applications directly to the environment and to crops necessitates precautionary measures to avoid unintended consequences. Further, the effects of using engineered nanomaterials (ENMs) in agricultural practices cascade throughout their life cycle and include effects from upstream-embodied resources and emissions from ENM production as well as their potential downstream environmental implications. Building on decades-long research in ENM synthesis, biological and environmental interactions, fate, transport and transformation, there is the opportunity to inform the sustainable design of nano-enabled agrochemicals. Here we perform a screening-level analysis that considers the system-wide benefits and costs for opportunities in which ENMs can advance the sustainability of crop-based agriculture. These include their on-farm use as (1) soil amendments to offset nitrogen fertilizer inputs, (2) seed coatings to increase germination rates and (3) foliar sprays to enhance yields. In each analysis, the nano-enabled alternatives are compared against the current practice on the basis of performance and embodied energy. In addition to identifying the ENM compositions and application approaches with the greatest potential to sustainably advance crop production, we present a holistic, prospective, systems-based approach that promotes emerging alternatives that have net performance and environmental benefits.