The dataset deposited here compiles all analytical and experimental files generated during the investigation of mercury (Hg) toxicity mitigation in transgenic soybean plants (Roundup Ready® and Intacta RR2 PRO™) treated with silica nanoparticles (SiO₂NPs) and sodium silicate (Na₂SiO₃). The collection integrates physicochemical characterization, elemental analyses, and advanced mass spectrometry datasets.The data include: Physicochemical Characterization: Files containing hydrodynamic diameter, polydispersity index (PDI), and zeta potential measurements for SiO₂ nanoparticles; Elemental and Speciation Data: Spreadsheets (Excel/CSV) with macro and micronutrient concentrations, silicon, and total mercury quantification in roots and leaves, including Hg(II) speciation analysis files; Imaging and Fractionation: Transmission electron microscopy (TEM) images demonstrating nanoparticle accumulation in tissues, and AF4–MALS–ICP-ToF-MS datasets containing fractionation profiles and elemental distribution; Metabolomics and Metallomics: HILIC–ESI–HRMS–ICP-MS/MS datasets, including peak tables, intensities, metabolite annotations, and aligned feature matrices; Statistical and Chemometric Files: Processed multivariate analysis files, including normalized matrices and outputs (PCA/PLS-DA) employed for metabolic interpretation.