INTRODUCTION: Trypanosoma cruzi is a protozoan parasite responsible for Chagas disease affecting millions globally. This parasite infects mammalian host cells, particularly macrophages. The interaction between T. cruzi and macrophages involves intricate signaling pathways mediated by pattern recognition receptors, which lead to the production of immune mediators, that are parasite-strain dependent and not completely understood. METHODS: We conducted an unbiased transcriptomic analysis of the immune response in mouse macrophages 24 h post-infection with the Y strain of T. cruzi using RNA-Seq and validated and compared the results using quantitative RT-PCR in macrophages infected with the Y and the VFRA T. cruzi strains. RESULTS: Bioinformatics analysis of the transcriptomics results evidenced a key role of Tlr2 and Tlr7 in the immune response against the parasite that was parasite-dependent. The Tlr2 signaling was more activated with the VFRA strain and the Tlr7 with the Y strain. Gene ontology analyses predicted a blockage in iron transport mediated by clathrin and the modulation of the extracellular matrix biosynthesis which were validated by RT-qPCR. The infection with the VFRA strain provoked the inhibition of ferritin which correlates with parasite proliferation. CONCLUSIONS: Our study recapitulates the knowledge on the response of macrophages and provides insights on the importance of TLR2 and TLR7, the iron metabolism, and the extracellular matrix in the infected macrophage that help to understand the molecular mechanisms underlying T. cruzi infection in macrophages in strains with different virulence. These findings are crucial for identifying novel therapeutic targets and advancing strategies to combat Chagas disease.