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Summary Dendritic cells (DCs) patrol tissues and transport antigens to lymph nodes to initiate adaptive immune responses. Within tissues, DCs constitute a complex cell population composed of distinct subsets that can exhibit different activation states and functions. How tissue-specific cues orchestrate DC diversification remains elusive. Here, we show that the small intestine included two pools of cDC2s originating from common pre-DC precursors: (1) lamina propria (LP) CD103+CD11b+ cDC2s that were mature-like proinflammatory cells and (2) intraepithelial cDC2s that exhibited an immature-like phenotype as well as tolerogenic properties. These phenotypes resulted from the action of food-derived retinoic acid (ATRA), which enhanced actomyosin contractility and promoted LP cDC2 transmigration into the epithelium. There, cDC2s were imprinted by environmental cues, including ATRA itself and the mucus component Muc2. Hence, by reaching distinct subtissular niches, DCs can exist as immature and mature cells within the same tissue, revealing an additional mechanism of DC functional diversification., Graphical abstract, Highlights • Epithelial colonization by gut cDC2s leads to their transcriptional reprograming • Unlike lamina propria cDC2s, intraepithelial cDC2s show an immature-like phenotype • Intraepithelial cDC2s trigger T cell hyporesponsiveness • The phenotype of intraepithelial cDC2s is imprinted by both retinoic acid and mucus, Gut cDC2s have been described to migrate into the epithelium, but whether this event modifies their phenotype is unknown. Rivera et al. show that upon epithelium colonization, cDC2s adopt an immature-like phenotype, revealing the existence of subtissular niches able to shape cDCs' fate and function.