We describe a comprehensive repository describing a collection of data from a range of studies investigating the molecular mechanisms of toxicity of glyphosate, the glyphosate-based herbicide commercial formulation Roundup, and a mixture of glyphosate and 5 other most frequently used pesticides (azoxystrobin, boscalid, chlorpyrifos, imidacloprid and thiabendazole) present as residues in food products in Europe. The data were obtained by analysing tissues from rats exposed to the pesticides for 90 days via drinking water. The administration of the mixture of six pesticides was chosen to mimic a possible human exposure scenario. We compared conventional methods used in regulatory toxicity studies to evaluate the safety of pesticide exposure (gross pathology, serum biochemistry) to new molecular profiling methods encompassing the analysis of the caecum and blood metabolome, liver transcriptome, liver DNA methylation, liver small RNA profiles, and caecum metagenome of the exposed animals. Altogether, these investigations provided in-depth molecular profiling in laboratory animals exposed to pesticides revealing metabolic perturbations that would remain undetected by standard regulatory biochemical measures. Our results highlight how multi-omics phenotyping can be used to improve the predictability of health risk assessment from exposure to toxic chemicals to better protect public health.