Alcohol is the most widely consumed legal drug, whereas cocaine is the illicit psychostimulant most commonly used in Europe. The combined use of alcohol and cocaine is frequent among drug-abuse consumers and leads to further exacerbation of health consequences compared to individual consumption. The pharmacokinetic and metabolic interactions leading to an increase in their combined toxicity still remains poorly understood. Here, the first metabolomics study of combined cocaine and ethanol chronic exposure effects is reported. A Liquid Chromatography strategy based on sample derivatization with 9-fluorenylmethyloxycarbonyl chloride and using a C18 column coupled to high resolution Mass Spectrometry (time of flight analyzer) was employed to analyze plasma from rats exposed intravenously to these drugs in a 52-min analysis. Using a combination of non-supervised and supervised multivariate analysis the metabolic differences between our experimental groups were explored and unraveled. A comparative analysis of the individual models and their variable importance in the projection values have shown that every experiment intervention includes a subset of specific metabolites. Eleven of these metabolites were annotated, where eight were unequivocally identified using standards and three were tentatively identified by matching the MS/MS spectra to libraries. The results demonstrated that the affected metabolic pathways were mainly those related to the metabolism of different amino acids.