Vitamin C (ascorbic acid) and vitamin B3 (niacin) have been extensively studied since the 20th century. In the area of stem cell biology, vitamin C has shown its direct impact towards homeostasis and epigenetic changes.1 Vitamin B3 aids in maintaining healthy intestinal homeostasis and reducing gut inflammation by participating in the rapamycin signaling pathway.2 In this study, vitamin C and vitamin B3 (600 and 1200 μg/ml) have been explored as potential new biomaterials to study their effects on four types of intestinal stem cells which are isolated from mice bearing different microbiota. We observed that C3H ASF and 129 ASF IL‐10 are more sensitive towards 600 μg/ml vitamin B3 and 1200 μg/ml vitamin C. The lowest growth rate and viability for all types of organoids was with 1200 μg/ml vitamin C. From qPCR analysis (quantitative Polymerase Chain Reaction analysis), MUC2 was upregulated for 129 ASF and C3H Conv when exposed to 600 μg/ml and 1200 μg/ml vitamin C. It suggests that large amounts of glycoprotein may be produced after adding high concentrations of vitamin C. Since inflammatory bowel disease has low level of MUC2, this finding may be helpful in restoring mucosal health by upregulating the MUC2 gene while altering patient's microbiota.3 These results are expected to have a positive translational impact because this bottom‐up strategy would be instrumental in developing Vitamin C and B3 based orally available therapeutic strategies and formula for advancing the fields of gastrointestinal regenerative medicine.