The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, involves administration of benznidazole (Bzn). Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active, although its mode of action is not fully understood. In the present work we used a non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn. Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols trypanothione, homotrypanothione and cysteine were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment. These metabolites included reduction products, fragments and covalent adducts of reduced Bzn linked to each of the major low molecular weight thiols: trypanothione, glutathione, γ-glutamylcysteine, glutathionylspermidine, cysteine and ovothiol A. Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI, were found within the parasites, but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected. Our data is indicative of a major role of the thiol binding capacity of Bzn reduction products in the mechanism of Bzn toxicity against T. cruzi. The unicellular parasite Trypanosoma cruzi infects humans, leading to Chagas disease, endemic in Central and South America and responsible for 13,000 annual deaths. Only two drugs have proven effective against Chagas, nifurtimox and benznidazole (Bzn). Bzn has the best safety and efficacy profiles and is thus used as first line treatment. Bzn is a pro-drug, and possesses a nitro group which needs to be enzymatically reduced within the parasite to become active. We have investigated for the first time, by means of mass spectrometry based metabolomics, the global changes to small metabolites that occur once Bzn enters the parasite. A decrease in the levels of several thiols, including cysteine and trypanothione, and an increase in gamma-glutamyl containing dipeptides were observed after treatment. Reduced metabolites of Bzn were also detected, together with numerous covalent conjugates of the drug combined with low molecular weight thiols and some non-thiol metabolites. Overall, Bzn treatment primarily affects thiol containing molecules in T. cruzi, and this interference with thiol metabolism contributes to the drug's mode of action.