Recent research indicates that mesenchymal stem cells (MSCs), known for their anti‐inflammatory and anti‐infectious properties, could be a promising alternative for treating inflammatory diseases such as inflammatory bowel disease (IBD). This study examined how MSCs and their derivatives, when cocultured with interleukin‐1β (IL‐1β)‐stimulated Caco‐2 cells, affect the expression of genes related to inflammation, microbes, and apoptosis. In the experiment, Caco‐2 cells were exposed to 10 ng/mL of IL‐1β for 24 h. MSCs were sourced from human bone marrow, adipose tissue (AD‐MSC), and menstrual blood. These MSCs and their conditioned medium (CM) were then cocultured with the IL‐1β‐induced Caco‐2 cells. After 48 h, gene expression levels were analyzed using real‐time PCR, and the data were statistically evaluated using T‐tests, U‐Mann–Whitney, and Tukey’s post hoc analyses. The results indicated that IL‐1β at 10 ng/mL was the optimal concentration for inducing Caco‐2 cells with the highest viability and minimal damage. Among the MSCs tested, AD‐MSCs were the most effective in regulating gene expression. Specifically, AD‐MSC treatment significantly reduced the mRNA expression of TNF‐α and IL‐1β, both of which are crucial in sustaining inflammatory responses (p ≤ 0.05). This study concludes that AD‐MSCs have superior effects compared to other MSC sources in modulating genes associated with inflammation, antibacterial effects, and apoptosis in an in vitro model of IBD using Caco‐2 cells.