The colonic mucus layer is organized as a two-layered system providing a physical barrier against pathogens and simultaneously harboring the commensal flora. The factors contributing to the organization of this gel network are not well understood. In this study, the impact of transglutaminase activity on this architecture was analyzed. Here, we show that transglutaminase TGM3 is the major TGM isoform expressed and synthesized in the colon. Furthermore, intrinsic extracellular TGM activity in the secreted mucus was demonstrated in vitro and ex vivo. Absence of this acyl-transferase activity resulted in faster degradation of the major mucus component the MUC2 mucin and changed the biochemical properties of mucus. Finally, TGM3-deficient mice showed an early increased susceptibility to DSS-induced colitis. Thus, these observations suggest that natural isopeptide cross-linking by TGM3 is important for mucus homeostasis and protection of the colon from inflammation, a suggested pre-stage of colon carcinoma.