The intestinal mucosa allows the residence of trillions of bacteria with which it interacts dynamically. To establish and maintain a mutually beneficial relationship, the mucosal immune system must enforce tolerance toward the vast non-pathogenic microbiota while simultaneously remaining reactive to potentially pathogenic microbes; the disruption of this delicate balance results in inflammatory bowel diseases. In this review, we describe advances in our understanding of regulatory mechanisms of the innate immune system and how these shape adaptive immune systems during steady-state and inflammatory processes in the intestinal mucosa.