Understanding potential uptake and biodistribution of engineered nanoparticles in soil-grown plants is imperative for toxicity and risk assessment considering the oral exposure of edibles by humans. Herein, we assessed potential influence of particle size (25, 50, and 250 nm) and concentration (0, 50, 100, 200, and 500 mg/kg-soil) of Copper oxide nanoparticles (CuONPs) on: (1) the root system architecture, and the physicochemical attributes of soil at the soil-root interface, (2) leading to Cu transport and accumulation in root, stem, leaf and seed in soybean (Glycine max cv Kowsar) grown for entire lifecycle of 120 days, and compared with soluble Cu²⁺ ions and water-only controls, and (3) performed a comparative assessment of total seed Cu levels in soybean with other valuable food sources for Cu intake and discussed its human health implications. Our findings showed particle size- and concentration-dependent influence of CuONPs on Cu uptake and tissue distribution in root, stem, leaf and seed in soybean. Alterations in root architecture (root dry weight, root length, root volume, and root area) were dependent on the Cu compound type, Cu concentrations, and their interactions (p<0.05), except for root density. Concentration-response relationships for all three sized CuONPs, and Cu²⁺ ions, were linear. CuONPs and Cu²⁺ ions had inhibitory effects on root growth and development. Overall, soybean responses to smallest size CuONPs-25 nm were higher for all parameters investigated compared to two larger sized CuONPs (50 nm, 250 nm) or Cu²⁺ ions. Cu uptake/bioaccumulation differed among soybean tissues in the order: root > leaf > stem > seed. Despite reduced root architecture and seed yield, our smallest size CuONPs-25 nm led to increased total seed Cu uptake compared to the larger sized CuONPs and Cu²⁺ ions tested. Our findings also suggest that soil amendment by CuONPs, more so by the smallest size CuONPs-25 nm, could significantly improve nutritional Cu value in soybean seed as reflected by % Daily Values (DV), and are rated “Good” to “Very Good” according to the “World’s Healthiest Foods” rating. However, until the potential toxicity and risk from consumption of soybean seed is characterized in humans, caution should be exercised when the Cu fortified seeds are used for daily human consumption when addressing Cu deficiency and associated illnesses, globally.