Soil organic matter plays a major role in determining the fate of the engineered nanomaterials (ENMs) in the soil matrix and effects on the residing plants. In this study, kidney bean plants were grown in soils varying in organic matter content and amended with 0-500mg/kg cerium oxide nanoparticles (nano-CeO2) under greenhouse condition. After 52days of exposure, cerium accumulation in tissues, plant growth and physiological parameters including photosynthetic pigments (chlorophylls and carotenoids), net photosynthesis rate, transpiration rate, and stomatal conductance were recorded. Additionally, catalase and ascorbate peroxidase activities were measured to evaluate oxidative stress in the tissues. The translocation factor of cerium in the nano-CeO2 exposed plants grown in organic matter enriched soil (OMES) was twice as the plants grown in low organic matter soil (LOMS). Although the leaf cover area increased by 65-111% with increasing nano-CeO2 concentration in LOMS, the effect on the physiological processes were inconsequential. In OMES leaves, exposure to 62.5-250mg/kg nano-CeO2 led to an enhancement in the transpiration rate and stomatal conductance, but to a simultaneous decrease in carotenoid contents by 25-28%. Chlorophyll a in the OMES leaves also decreased by 27 and 18% on exposure to 125 and 250mg/kg nano-CeO2. In addition, catalase activity increased in LOMS stems, and ascorbate peroxidase increased in OMES leaves of nano-CeO2 exposed plants, with respect to control. Thus, this study provides clear evidence that the properties of the complex soil matrix play decisive roles in determining the fate, bioavailability, and biological transport of ENMs in the environment.