Mucosal barrier surfaces of the mammalian body are frequent sites of pathogen colonization or entry and are also densely colonized with trillions of normally beneficial microbes, termed the microbiota. Therefore, it is paramount that the host immune system recognizes these microbes and is capable of differentiating between them. To this end, a multitude of mechanisms have evolved to carefully balance the need for immune activation in the face of infections while maintaining an appropriate level of tolerance to protect both the host and the beneficial microbes from hyperactivation. These mechanisms include the deployment of an emerging class of tissue-resident innate immune cells, innate lymphoid cells (ILCs), that are enriched at mucosal barriers such as the lungs and intestines, and are critical mediators of tissue homeostasis, tolerance, repair, and innate immunity. Recent findings have provided insight into the regulation of these cells and their interactions, not only with microbes, both commensal and foreign, but also with other systems of the body to prevent disease and promote tissue health. Here, we discuss recent findings in the regulation and function of ILCs, including a focus on their interactions with bodily systems, such as the nervous system, and how these interactions affect their functionality in states of health, infection, and disease.