Pesticides constitute a category of chemical products intended specifically for the control and mitigation of pests. With their constant increase in use, the risk to human health and the environment has increased proportionally due to occupational and environmental exposure to these compounds. The use of these chemicals is associated with several toxic effects related to acute and chronic toxicity, such as infertility, hormonal disorders and cancer. The present work aimed to study the metabolic profile of individuals occupationally exposed to pesticides, using a metabolomics tool to identify potential new biomarkers. Metabolomics analysis was carried out on plasma and urine samples from individuals exposed and non-exposed occupationally, using liquid chromatography coupled with mass spectrometry (UPLC-MS). Non-targeted metabolomics analysis, using principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) or partial least squares discriminant orthogonal analysis (OPLS-DA), demonstrated good separation of the samples and identified 21 discriminating metabolites in plasma and 17 in urine. The analysis of the ROC curve indicated the compounds with the greatest potential for biomarkers. Comprehensive analysis of the metabolic pathways influenced by exposure to pesticides revealed alterations, mainly in lipid and amino acid metabolism. This study indicates that the use of metabolomics provides important information about complex biological responses.