Trypanosoma cruzi, the causative agent of Chagas disease, is a genuine parasite with a tremendous genetic diversity and a complex life cycle. Scientists have studied this disease for more than 100 years, and Chagas disease drug discovery has been a mainstay due to the absence of an effective treatment. Technical advances in several areas have contributed to a better understanding of the complex biology and life cycle of this parasite with the aim of designing the ideal profile of both drug and therapeutic options to treat CD. Here, we present T. cruzi Arequipa strain (MHOM/Pe/2011/Arequipa) as an interesting tool for CD drug discovery. We have characterized acute-phase parasitaemia and chronic-phase tropism in BALB/c mice, and we have determined the in vitro and in vivo benznidazole resistance profile of the different morphological forms of this strain. The tropism of this strain makes it an interesting tool for the screening of new compounds with a potential anti-Chagas profile for the treatment of this disease.