Some of the interactions between prokaryotes and eukaryotes are mediated by a molecular dialogue between microbial MAMPs and host PRRs. Bacteria-derived peptidoglycan, which possesses all the characteristics of a MAMP, is detected by membrane-bound or cytosolic PRRs belonging to various families of proteins in both animals and plants (PGRP, Nod, Lys-M...). If the identity and the epistatic relationship between the downstream components of the signaling cascades activated upon PGN/PRR interactions are well characterized, little is known about the subcellular events requires to translate these early sensing steps into downstream target gene transcription. Using a model of Drosophila enteric infection, we show that gut-associated bacteria can induce PGRP-LE intracellular aggregation. Observed in both enterocytes and entero-endocrine cells, these aggregates were found to co-localize with the early endosome marker Rab5. In vivo functional analysis further demonstrates that, whereas some PGRP-LE target genes, such as antimicrobial peptides, can be activated independently of Rab5, other such as the PGRP-SC1 amidase, need the combined action of PGRP-LE and Rab5 to be transcribed. These results demonstrate how by using different intracellular signaling routes, the same ligand/receptor complex can activate different target genes in the same cell.