Phosphorylation is an important event in cell signaling that is modulated by kinases and phosphatases. In T. cruzi, the etiological agent of Chagas disease, approximately 2% of the genome comprises protein kinases. This parasite has a heteroxenic life cycle with four different development stages. In the midgut of triatomine, epimastigotes differentiate into metacyclic trypomastigotes in a process known as metacyclogenesis. This process can be reproduced in vitro by submitting parasites to nutritional stress (NS). Aiming to contribute to the elucidation of mechanisms that trigger metacyclogenesis, we applied super-SILAC (super-stable isotope labeling by amino acids in cell culture) and LC-MS/MS to analyze different points during NS. This analysis resulted in the identification of 4,205 protein groups and 3,643 phosphopeptides with the location of 4,846 phosphorylation sites. Several phosphosites were considered modulated along NS and are present in proteins associated with various functions, such as fatty acid synthesis and the regulation of protein expression, reinforcing the importance of phosphorylation and signaling events to the parasite. These modulated sites may be triggers of metacyclogenesis.