In vitro models of the gut-microbiome axis are in high demand. Conventionally, intestinal monolayers grown on Transwell culture setups are used to test the effects of commensals/pathogens on the integrity of the barrier, both under homeostatic and pathophysiological conditions. While such models remain valuable for deepening our understanding of host-microbe interactions, often they lack key biological components that mediate this intricate crosstalk. Here, we develop a 3D in vitro model of the vertebrate intestinal epithelium, interfaced with immune cells surviving in culture for over three weeks, and demonstrate its applicability to proof-of-concept studies of host-microbe interactions. More specifically, we describe the establishment of stable host-microbe co-cultures and show functional and morphological changes in the intestinal barrier induced by the presence of commensal bacteria. Finally, we provide evidence that our vertebrate 3D gut models can be used as platforms to test host-microbe-parasite interactions. Exposure of gut-immune-bacteria co-cultures to helminth ‘excretory/secretory products’ (ESP) induces in vivo-like up-/down-regulation of certain cytokines. These findings support the robustness of our modular in vitro cell systems for investigating the dynamics of host-microbe crosstalk and pave the way toward new approaches for systems biology studies of pathogens that cannot be maintained in vitro, such as parasitic helminths.