Macrophages reside in a dense cellular network in the intestinal muscularis externa, and there is emerging evidence that the functionality of these cells determines the local microenvironment. Inflammatory responses during intestinal diseases change the homeostatic functionality of these cells causing inflammation and intestinal dysmotility. Such disturbances are not only induced by a change in the cellular composition in the intestinal muscularis but also by an altered crosstalk with the peripheral and central nervous system. In this review, we summarize the role of muscularis macrophages in the intestine in homeostasis and inflammation. We compare the functionality, the phenotype, and the origin of muscularis macrophages to their neighboring counterparts within the different layers of the intestine. We outline the cellular crosstalk with the enteric and the peripheral nervous system and summarize the current therapeutic approaches to modulate the functionality of these phagocytes.