Abstract Background Biallelic anterior gradient 2 (AGR2) loss-of-function variants cause infantile-onset inflammatory bowel disease, alongside histological changes of the gastrointestinal epithelium. The underlying mechanisms on epithelial development and function are not understood. Methods We conducted single-cell RNA-sequencing of gastrointestinal biopsies and organoids from AGR2-deficient patients. Organoids were used for functional investigation of the epithelium and mucus layer by flow cytometry, confocal microscopy, and using a microfluidic organ-chip. Multiplexed imaging was used to characterise intestinal metaplasia in the antrum. Results AGR2-deficiency caused region-specific changes in epithelial cell populations. In the gastric antrum, AGR2-deficiency led to defective epithelial cell differentiation into premalignant metaplastic enterocytes associated with an up-regulation of gastric cancer markers. In the colon, despite a histological depletion of goblet cells, single-cell analysis demonstrated an over-abundance of goblet cells in AGR2-deficiency, exhibiting high ER-stress. We identified defective processing of MUC2 and reduced MUC2 storage in goblet cells without signs of crinophagy, suggesting a stress-induced secretion. Similar to AGR2-deficiency, in ulcerative colitis, goblet cells revealed high ER-stress and no reduction in cell numbers. Conclusion Our data highlight AGR2-deficiency as a genetic model of precancerous intestinal metaplasia in the gastric antrum. Apparent colonic goblet cell depletion in AGR2-deficiency and in ulcerative colitis is a histological artefact, representing a reduction of stored mucins in goblet cells via stress-induced mucus secretion.