The intestinal epithelium plays an essential role in the balance between tolerant and protective immune responses to infectious agents. In vitro models do not typically consider the innate immune response and gut microbiome in detail, so these models do not fully mimic the physiologic aspects of the small intestine. We developed and characterized a long‐term in vitro model containing enterocyte, goblet, and immune‐like cells exposed to a synthetic microbial community representative of commensal inhabitants of the small intestine. This model showed differential responses toward a synthetic microbial community of commensal bacterial inhabitants of the small intestine in the absence or presence of LPS from Escherichia coli 0111:B4. Simultaneous exposure to LPS and microbiota induced impaired epithelial barrier function; increased production of IL‐8, IL‐6, TNF‐α, and C‐X‐C motif chemokine ligand 16; and augmented differentiation and adhesion of macrophage‐like cells and the overexpression of dual oxidase 2 and TLR‐2 and ‐4 mRNA. In addition, the model demonstrated the ability to assess the adhesion of specific bacterial strains from the synthetic microbial community—more specifically, Veillonella parvula—to the simulated epithelium. This novel in vitro model may assist in overcoming sampling and retrieval difficulties when studying host‐microbiome interactions in the small intestine.—Calatayud, M., Dezutter, O., Hernandez‐Sanabria, E., Hidalgo‐Martinez, S., Meysman, F. J. R., Van de Wiele, T. Development of a host‐microbiome model of the small intestine. FASEB J. 33, 3985–3996 (2019). http://www.fasebj.org