Background Intestinal fibrosis, a complex complication of colitis, is characterized by excessive extracellular matrix (ECM) deposition. Estrogen receptor (ER) beta may play a role in regulating this process.Methods Intestinal tissue samples from stenotic and nonstenotic regions were collected from Crohn's disease (CD) patients. RNA sequencing was conducted on a mouse model to identify differentially expressed mRNAs. Histological, immunohistochemical, and semiquantitative Western blotting analyses were employed to assess ECM deposition and fibrosis. The roles of relevant pathways in fibroblast transdifferentiation, activity, and migration were examined.Results Estrogen receptor beta expression was found to be downregulated in the stenotic intestinal tissue of CD patients. Histological fibrosis score, collagen deposition, and profibrotic molecules in the colon of an intestinal fibrosis mouse model were significantly decreased after activation of ER beta. In vitro, ER beta activation alleviated transforming growth factor (TGF)-beta-induced fibroblast activation and migration, as evidenced by the inhibition of col1 alpha 1, fibronectin, alpha-smooth muscle actin (alpha-SMA), collagen I, and N-cadherin expression. RNA sequencing showed that ER beta activation affected the expression of genes involved in ECM homeostasis and tissue remodeling. Enrichment analysis of differentially expressed genes highlighted that the downregulated genes were enriched in ECM-receptor interaction, TGF-beta signaling, and Toll-like receptor (TLR) signaling. Western blotting confirmed the involvement of TGF-beta/Smad and TLR4/MyD88/NF-kappa B signaling pathways in modulating fibrosis both in vivo and in vitro. The promoter activity of TGF-beta 1 and TLR4 could be suppressed by ER beta transcription factor.Conclusion Estrogen receptor beta may regulate intestinal fibrosis through modulation of the TGF-beta/Smad and TLR4/MyD88/NF-kappa B signaling pathways. Targeting ER beta activation could be a promising therapeutic strategy for treating intestinal fibrosis. Imagine your gut is like a garden hose. In Crohn's disease, parts of this "hose" get narrow and blocked. Scientists found less of a helpful protein, ER beta, in these narrow areas. In an experiment with mice, boosting ER beta lessened the gut damage and reduced the buildup of collagen-the "blockage" in our hose analogy. Also, ER beta calmed overactive cells causing these issues, acting like a peacemaker. This protein "talks" to cells through channels called TGF-beta/Smad and TLR4/NF-kappa B, telling them to relax. This could be a new way to tackle such gut problems! Graphical AbstractSummary of the underlying mechanisms by which estrogen receptor (ER) beta inhibits intestinal fibrosis through TGF-beta/Smad and TLR4/Myd88/NF-kappa B pathway.