The insect gut is lined by a protective, chitinous peritrophic matrix (PM) that separates immunoreactive epithelial cells from microbes present within the luminal contents. Tsetse flies (Glossina spp.) imbibe vertebrate blood exclusively, and can be exposed to foreign microorganisms during the feeding process. We employed RNAi-based reverse genetics to inhibit the production of a structurally robust PM, and then observed how this procedure impacted infection outcomes following per os challenge with exogenous bacteria (Enterobacter sp. and Serratia marcescens strain Db11) and parasitic African trypanosomes. Enterobacter and Serratia proliferation was impeded in tsetse that lacked an intact PM because these flies expressed the antimicrobial peptide gene, attacin, earlier in the infection process than did their counterparts that housed a fully developed PM. Following challenge with trypanosomes, attacin expression was latent in tsetse that lacked an intact PM and these flies were thus highly susceptible to parasite infection. Our results suggest that IMD signaling pathway effectors, as opposed to reactive oxygen intermediates, serve as the first line of defense in tsetse’s gut following the ingestion of exogenous microorganisms. Furthermore, tsetse’s PM is not a physical impediment to infection establishment, but instead serves as a barrier that regulates the fly’s ability to immunologically detect and respond to the presence of these microbes. Collectively, our findings indicate that effective insect antimicrobial responses depend largely upon the coordination of multiple host and microbe-specific developmental factors.