The use of 3D-small intestinal organoid models (enteroids) enables investigation of chemosensing mechanisms for nutrients, bioactive substances and metabolites, with the intestinal epithelium. Enteroids are non-cancerous mini-guts grown from stem cells that contain all different types of epithelial cells, including enterocytes, goblet cells, enteroendocrine cells, and Paneth cells. Therefore, enteroids represent a genotypically and phenotypically superior model compared to cell lines. Nevertheless, one challenge in using enteroids is the difficulty in accessing the luminal (or apical) surface of the epithelium, which is enclosed in the enteroids’ interior. Therefore, we generated an enteroid mouse model (C57BL/6) in which the luminal surface of the enteroid faces outward (apical-out). Apical-out enteroids were created by removing extracellular protein matrix (ECM), thereby disrupting ECM-integrin receptor interactions. Flipping enteroid polarity (from apical-in to apical-out) was visualized by fluorescence confocal microscopy, in which the nuclei, actin cytoskeleton in the microvilli brush border, and fucose units in the mucus layer were stained. Additionally, we showed that apical-out enteroids were less sensitive to exposure of phenolic compounds, likely due to the mucus layer surrounding the apical brush-border. Based on gene expression of epithelial cell markers, we demonstrated that apical-out jejunal enteroids show better resemblance to jejunal tissue of C57BL/6 mice compared to apical-in jejunal enteroids. Altogether, apical-out enteroids provide a better mimic of the gastrointestinal lining compared to conventional apical-in enteroids. This model seems suitable to study the interactions between nutrients and their bioactive metabolites with nutrient sensing receptors expressed on specialized intestinal cell types. Consequently, their physiological effects such as secretion of gut hormones, antimicrobial lysozymes or protective mucus can be unveiled.