Trypanosoma cruzi invades non-professional phagocytic cells by subverting their membrane repair process, which is dependent on membrane injury and cell signaling, intracellular calcium increase and lysosome recruitment. Cells lacking Lysosome Associated Membrane Proteins 1 and 2 are less permissive to parasite invasion, however more prone to parasite intracellular multiplication. Several passages through a different intracellular environment can significantly change T. cruzi’s gene expression profile. We evaluated whether one single passage through LAMP deficient (KO) or wild type (WT) fibroblasts could influence invasion ability of T. cruzi Y strain trypomastigotes in L6 myoblasts and WT fibroblasts. Our results regarding their biological behavior clearly indicated that parasites released from WT cells (TcY-WT), LAMP1/2 KO cells (TcY-L1/2-/-) or LAMP2 KO (TcY-L2-/-) cells are distinct from each other. Since these alterations most likely would reflect differences among parasite surface molecules, we also evaluated their proteome. We identified few protein complexes, membrane and secreted proteins regulated in our dataset. Among those, some members of MASP, mucins, trans-sialidases and gp63 proteins family, which are known to play an important role during parasite infection and could correlate to TcY-WT, TcY-L1/2-/- and TcY-L2-/- biological behavior.