With increasing use, manufactured nanomaterials (MNMs) may enter soils and impact agriculture. Herein, soybean (Glycine max) was grown in soil amended with either nano-CeO (0.1, 0.5, or 1.0gkg soil) or nano-ZnO (0.05, 0.1, or 0.5gkg soil). Leaf chlorosis, necrosis, and photosystem II (PSII) quantum efficiency were monitored during plant growth. Seed protein and protein carbonyl, plus leaf chlorophyll, reactive oxygen species (ROS), lipid peroxidation, and genotoxicity were measured for plants at harvest. Neither PSII quantum efficiency, seed protein, nor protein carbonyl indicated negative MNM effects. However, increased ROS, lipid peroxidation, and visible damage, along with decreased total chlorophyll concentrations, were observed for soybean leaves in the nano-CeO treatments. These effects correlated to aboveground leaf, pod, and stem production, and to root nodule N fixation potential. Soybeans grown in soil amended with nano-ZnO maintained growth, yield, and N fixation potential similarly to the controls, without increased leaf ROS or lipid peroxidation. Leaf damage was observed for the nano-ZnO treatments, and genotoxicity appeared for the highest nano-ZnO treatment, but only for one plant. Total chlorophyll concentrations decreased with increasing leaf Zn concentration, which was attributable to zinc complexes-not nano-ZnO-in the leaves. Overall, nano-ZnO and nano-CeO amended to soils differentially triggered aboveground soybean leaf stress and damage. However, the consequences of leaf stress and damage to N fixation, plant growth, and yield were only observed for nano-CeO.