The intestinal epithelium contains secretory and absorptive cell lineages that develop from undifferentiated progenitor cells. Despite the collective importance of these cells to host responses against microbial invaders, little is known about the contributions of immune responses in individual cell types to the maintenance of intestinal homeostasis. In this study, we asked how inhibition of immune pathway activity exclusively in progenitor cells, or in differentiated enterocytes, affects midgut homeostasis in adult Drosophila. We found that blocking immune activity in enterocytes rendered flies more tolerant of Vibrio cholerae infection, had negligible effects on the gut bacterial microbiome, and significantly affected metabolism. In contrast, inhibition of immune activity in progenitors rendered flies less tolerant of Vibrio infections, modified host association with Lactobacillus symbionts, and blocked growth and renewal in the midgut epithelium. Together, these data uncover substantial cell type-specific contributions of epithelial immunity to adult intestinal homeostasis.