The Capuchins settled in San Giovanni Rotondo in 1540, and erected a cross on a small terrace on the slopes of the Mantenero. This cross can still be seen from the churchyard today.
Padre Pio first went to San Giovanni Rotondo for a very brief spell (28 July - 5 August 1916) due to the usual health reasons, but on 4 September the same year he was back there. Apart from a few brief spells away due to military and spiritual reasons, the monastery was to become his fixed abode from then on.
It was here that the stigmata appeared and numerous spiritual events occurred. One worth particular mention here is linked with the subject of the nativity. This is how Padre Raffaele from Sant' Elia a Pianisi described the event: "I was sleeping in a narrow cell, directly opposite no 5, where Padre Pio was. I do not know why - maybe because of the heat - but around midnight I woke up in terror. The corridor was dark, the darkness broken only be the dim light coming from an oil lamp. Just as I was about to leave my cell, Padre Pio walked past, coming back from the chancel where he had been praying. It was midnight. Padre Pio, glowing with light and carrying the Infant Jesus on his arm, walked past slowly murmuring prayers. He was walking in front of me, radiant with light, but did not notice my presence. "
The church of Santa Maria delle Grazie was opened in 1959, and the story is told how on that occasion Padre Pio exclaimed to his fellow friars "What have you made? A matchbox?" He already knew that a large building would be needed to hold the multitudes of the "faithful that would answer his call".
His wish came true on 16 May 1993, when building work began on an enormous new church designed by the architect Renzo Piano.