Understanding the complex mechanisms involved in plant response to nanoparticles is indispensable in assessing the impact of nano-pollutants on environment. The present study compares the phytotoxicity of three different metal-based nanoparticles (Al2O3, ZnO, and Ag) in soybean seedling at proteome level. Plant growth, rigidity of roots, and root cell viability were markedly affected by ZnO- and Ag-NPs stress; while, Al2O3-NPs challenged soybean maintained normal seedling growth like control. Moreover, severe oxidative burst was evident in ZnO-NPs and Ag-NPs treatments. Gel-free proteomic analysis of NPs stressed soybean roots revealed 104 commonly changed proteins primarily associated with secondary metabolism, cell organization, and hormone metabolism. Oxidation-reduction cascade related genes, such as GDSL motif lipase 5, SKU5 similar 4, galactose oxidase, and quinone reductase were up-regulated in Al2O3-NPs challenged roots and down-regulated in ZnO- and Ag-NPs treatments. In comparison to root, 16 common proteins were found to be significantly changed in leaves of NPs exposed soybean that were predominantly associated to photosystem and protein degradation. The proteomic findings suggest that high abundance of proteins involved in oxidation-reduction, stress signaling, hormonal pathways related to growth and development might be the principal key for optimum growth of soybean under Al2O3-NPs stress. (C) 2015 Elsevier B.V. All rights reserved.