Trypanosoma cruzi is an obligate intracellular parasite transmitted to vertebrate hosts by blood-sucking insects. Molecules present in parasites and mammalian cells allow the recognition and parasite internalization. Metallic ions play an essential role in the establishment and maintenance of hostparasite interaction. However, little is known about how parasites handle with essential and nonessential metal quotas. This study aimed to investigate the influence of metal ions on the biological processes of T. cruzi infected cells. Infected cells were incubated with ZnCl2, CdCl2, and HgCl2 for 12 h and labeled with different specific dyes to investigate the cellular events related to intracellular parasite death and elimination. Infected host cells and parasite’s mitochondria underwent functional and structural disorders, in addition to parasite’s DNA condensation and pH decrease on host cells, which led to parasite death. Further investigations suggested that lysosomes were involved in pH decrease and the double membrane of the endoplasmic reticulum formed vacuoles surrounding damaged parasites, which indicate the occurrence of autophagy for parasite elimination. In conclusion, low concentrations of nonessential and essential metals cause a series of damage to Trypanosoma cruzi organelles, leading to its loss of viability, death, and elimination, with no removal of the host cells.