Although since the 20s there had been a growing number of pilgrims climbing Mount Gargano and the inadequacy of the Church of Santa Maria delle Grazie to accommodate this crowd (so much so that Padre Pio often had to celebrate outdoors), the works for the Sanctuary began only in 1956.
The construction took shape under the careful guidance of the architect Giuseppe Gentile di Boiano and was consecrated on 1 July 1959. It consists of three naves, with the central one dominated by the imposing mosaic of the apse, created by the Vatican school, which depicts the icon of the Madonna delle Grazie in the glory of the angels and of Saint Pio, the intermediary between Mary and suffering humanity.
In the presbytery, a new altar consecrated on 13 December 2008 replaced the one on which Padre Pio celebrated the Eucharist from 1959 until 22 September 1968. The old Eucharistic table was "set" like a precious gem in the main altar, at the base of the tabernacle.
The side naves are enriched by nine minor altars, and above all host the wooden statue of the Madonna delle Grazie together with two recent mosaics depicting Saint John Paul II and the Blessed Mother Teresa of Calcutta, with the related relics.