The monastery, named after a Catholic title for Mary, is located on the Vatican hill inside the Vatican Gardens and near the Aquilone fountain. The building was erected between 1992 and 1994 in place of an administrative building of the Vatican police. Its structure is incorporated into the Leonine walls. The building is divided in two parts: The western chapel (two floors and rectangular in shape) and the eastern community rooms and monastic cells (rectangular in shape and, on the Aquilone fountain's side, with four floors, with 12 monastic cells on the second and third floors, and a refectory, store, kitchen, infirmary, archives and an office-studio on the ground and lower ground floors). Adjacent to the monastery is a fruit and vegetable garden.
Mater Ecclesiae was founded by John Paul II in order to have a monastic group of nuns inside Vatican City, who pray for the pope and the Church. This task was at the beginning within the responsibilities of the nuns of the order of Saint Clare. This assignment however was shifted every five years to another female religious order. With the start of renovation works in November 2012, the last nuns moved out.