Metabolomics is an emerging tool to understand the potential implications of nanotechnology, particularly for agriculture. Although molybdenum (Mo) is a known plant micronutrient, little is known of its metabolic perturbations. Here, corn and wheat seedlings were exposed to MoO 3 nanoparticles (NPs) and the corresponding bioavailable Mo 6+ ion at moderate and excessive levels through root exposures. Physiologically, corn was more sensitive to Mo, which accumulated up to 3.63 times more Mo than wheat. In contrast, metabolomics indicated 21 dysregulated metabolites in corn leaves and 53 in wheat leaves. Five more metabolomic pathways were perturbed in wheat leaves compared to corn leaves. In addition to the overall metabolomics analysis, we also analyzed individual metabolite classes (e.g., amino acids, organic acids, etc.), yielding additional dysregulated metabolites in plant tissues: 7 for corn and 7 for wheat. Most of these were amino acids as well as some sugars. Additional significantly dysregulated metabolites (e.g., asparagine, fructose, reduced glutathione, mannose) were identified in both corn and wheat, due to Mo NP exposure, by employing individual metabolite group analysis. Targeted metabolite analysis of individual groups is thus important for finding additional significant metabolites. We demonstrate the value of metabolomics to study early stage plant responses to NP exposure.