The gut is composed of a single layer of intestinal epithelial cells (IECs) lines between the external environment and immune compartment. The epithelial monolayer physically impedes the penetration of microorganisms, but it can also interact with them to maintain homeostasis. Innate immune sensing mechanisms, such as the expression of pattern recognition receptors (PRRs), are essential for segregating between commensal bacteria and pathogens by IECs. Toll-like receptors (TLRs) are PRRs that can recognize a wide range of microbial signals on both apical and basolateral epithelial surfaces and enable the polarized response of either tolerogenic or immune responses by IECs. Recently TLR2 expression was identified on the small intestine (SI) intestinal stem cells (ISC) by single-cell RNA sequencing (scRNA-seq). However, it is unclear how recognition of microbial signals in the stem cell niche affects ISCs self-renewal and differentiation therefore, examination of TLR2 expression and function in ISCs is important. Here, we found that TLR2 exhibits a segmental expression pattern on SI crypts under homeostasis, following the microbiota abundance. Second, we showed that TLR2 signaling has an exclusive functional response on the apical side by in-vitro activation assays of TLR2 on stem-enriched epithelial monolayer. Lastly, in-vivo TLR2 genetic ablation showed differences in IECs differentiation. Paneth cell differentiation was blocked, accompanied by goblet/Paneth intermediate population accumulation, which suggests the involvement of TLR2 in Paneth cell maturation under homeostasis. These findings reveal the important role of TLR2 as an innate immune sensor on IECs and its involvement in regulating the ISCs pool and IECs differentiation.