Abstract There is an urgent need to develop new drugs against Chagas’ disease. In addition, the mechanisms of action of existing drugs have not been completely worked out at the molecular level. High throughput approaches have been demonstrated to be powerful tools not only for understanding the basic biology of Trypanosoma cruzi, but also for the identification of drug targets such as proteins or pathways that are essential for parasite infection and survival within the mammalian host. Here, we have applied these tools towards the discovery of the effects of two organometallic compounds with trypanocidal activity, Pd–dppf–mpo and Pt–dppf–mpo, on the transcriptome and proteome of T. cruzi epimastigotes. These approaches have not yet been reported for any other prospective metal-based anti T. cruzi drug. We found differentially expressed transcripts and proteins in treated parasites. Pd–dppf–mpo treatment resulted in more modulated transcripts (2327 of 10 785 identified transcripts) than Pt–dppf–mpo treatment (201 of 10 773 identified transcripts) suggesting a mechanism of action for Pd–dppf–mpo at the transcriptome level. Similar numbers of differentially expressed proteins (342 and 411 for Pd–dppf–mpo and Pt–dppf–mpo respectively) were also observed. We further functionally categorized differentially expressed transcripts and identified cellular processes and pathways significantly impacted by treatment with the compounds. Transcripts involved in DNA binding, protein metabolism, transmembrane transport, oxidative defense, and the ergosterol pathways were found to be modulated by the presence of the compounds. Our transcriptomic dataset also contained previously validated essential genes. These data allowed us to hypothesize a multimodal mechanism of action for the trypanocidal activity of Pd–dppf–mpo and Pt–dppf–mpo, and a differential contribution of the metal moiety of each compound.