The dataset deposited here compiles all files generated during the experiment that investigated the effects of silver nanoparticles (AgNPs) and silver nitrate (AgNO₃) on the metabolism of transgenic soybean plants (RR and Intacta genotypes). The collection integrates different types of analytical data used for chemical characterization, metabolic profiling, and multivariate statistical interpretation. Purpose: The purpose of this dataset is to make available, in an organized and reproducible manner, all raw and processed files used in the metabolomics analyses of the study. These files allow replication of the statistical analyses, validation of the results, and future reprocessing using new computational approaches. Nature of the data: The data include: ¹H NMR spectra (zipped folders containing spectra from leaf, stem, and root samples), used for metabolite identification and relative quantification. LC–MS spreadsheets (negative mode) containing peak lists, intensities, and m/z values for leaf, stem, and root samples. Processed MetaboAnalyst files, including normalized tables, transformed data, and working matrices used for multivariate statistical analyses. Bucketed tables (AMIX) corresponding to NMR data employed in PCA and other chemometric evaluations. Spreadsheets of relative signal integration, generated after NMR spectral processing. Scope of the dataset: The dataset covers three plant tissues (leaf, stem, and root), enabling the assessment of metabolic differences between genotypes and treatments. It includes raw files as well as analysis-ready matrices, supporting studies in toxicity, ecophysiology, metabolomics, agricultural nanotechnology, and the complete reproducibility of the project’s findings.