Over 100 million women worldwide are currently on progesterone-based contraceptives to improve their health outcomes through reduced maternal mortality and family planning. In addition to their role in reproduction, progesterone-based compounds modulate immune responses throughout the body, particularly at mucosal sites. By binding to receptors located in immune cells, including natural killer cells, macrophages, dendritic cells, and T cells, as well in non-immune cells, such as epithelial and endothelial cells, progesterone-based compounds alter cellular signaling and activity to affect the outcome of infections at diverse mucosal sites, including the genital, gastrointestinal, and respiratory tracts. As the use of progesterone-based compounds, in the form of contraceptives and hormone-based therapies, continue to increase worldwide, greater consideration should be given to how the immunomodulatory effects these compounds alter the outcome of diseases at mucosal sites beyond the reproductive tract, which has profound implications for women's health.