There is inadequate understanding of the environmental fate and effects of engineered nanoparticles, including nanoceria. Also, knowledge about the influence of environmental factors on the bioavailability of these particles and resulting impacts on the nutritional quality of crops is limited. Alterations in mineral and macromolecular composition of some grains and fruits under nanoceria exposure have been reported recently; however, the cellular mechanisms associated with the effects are unknown. Here, we show that the impact of nanoceria at 62.5 to 500 mg/kg soil on kidney bean (Phaseolus vulgaris) productivity and seed quality are influenced by soil organic matter content. Seeds obtained from plants exposed to nanoceria at 125 mg/kg showed unique and contrasting response in terms of nutritional quality under varying soil organic matter content. Additionally, quantitative proteomic analysis provides evidence for dose-dependent down-regulation of some major proteins associated with nutrient storage and carbohydrate metabolism, including phaseolin and lectins in the exposed seeds. This study suggests that nCeO2 exposure negatively impacts the nutritional quality of kidney beans. This altered seed quality may have significant implications for food production and human health.