The metabolic adaptability of Trypanosoma cruzi, the causative agent of Chagas disease, and other trypanosomatids across their life cycle stages is a defining feature of their biology and pathogenicity. Studying parasite and host cell metabolic profiles during infections is crucial to understanding disease progression and developing targeted therapeutic interventions. Traditionally, researchers have faced limitations in effectively capturing the dynamic nature of metabolic shifts in real time, hindering our ability to unravel the complex interplay between the host and the pathogen. Approaching these questions requires a high-throughput technique capable of assessing the metabolic changes and preferences of both the parasite and the host cell under physiological conditions in infected cells and tissues. A novel analytical technique that promises to push forward our understanding of metabolic profiles during Trypanosoma cruzi infections has now been developed. Here, we describe the potential to exploit the Single-Cell Energetic Metabolism by Profiling Translation Inhibition (SCENITH™) to examine the energetic metabolism of T. cruzi during its distinct developmental stages—epimastigote, trypomastigote, and amastigote—allowing to unveil the metabolic shifts that underpin their survival and proliferation in diverse host environments. Additionally, SCENITH allows to study how infected host cells’ metabolism changes in the presence of parasites. The variability in metabolic pathways offers a unique perspective for identifying and developing stage-specific drug targets, presenting opportunities for more effective therapeutic interventions.