The vector potential of houseflies to transmit Aeromonas spp. and other enteropathogens from septic environments has been well investigated. However, the interactions between enteropathogens and the barrier-mediated, physical defenses within flies have been understudied. We examined the temporal and spatial fate of ingested GFP-tagged motile and non-motile strains of Aeromonas within the digestive tract (crop, stomach, midgut) of laboratory-reared houseflies. Food consumed by houseflies is normally stored in the crop, and subsequently is redirected into the stomach and midgut while inside a double-layered type II peritrophic matrix (PM). The PM is continually extruded, and moves posteriorly like a conveyor belt, carrying materials along with it. As it progresses distally, the inner layer of the PM compresses ingested substances into fecal pellets which are later excreted. In Aeromonas-fed flies, many live (GFP+) bacteria apparently were adhering to the luminal surfaces of the crop and inner PM, irrespective of motility. Concurrently, the materials which would later form the food pellets (mainly some digested bacteria and freed GFP) passed by, while non-adherent, live bacteria were able to swim freely within the crop and PM lumen around the anterior and medial section of midgut. Ultimately, in the posterior section of the midgut (at the hind gut junction), all bacteria encounter the same fate, being compressed into a fecal pellet, lysed (digested) and excreted. Thus, anterior station transmission of viable pathogens via vomitus is probably more significant to vector potential since it is unlikely that significant numbers of viable bacteria are released in the feces.