At the heart of the vast and harmonious convent stands the church, built in the 15th century and dedicated to St Francis. Today there remains of the ancient building the beautiful and solemn Gothic apse, the rest of the church is the fruit of the alterations made in the second half of the 19th century. The church incorporates on its left side the 16th century oratory built by the Perugian architect Giangaleazzo Alessi and dedicated to the Immaculate Conception.

At one time, the church was richly endowed with art works of Perugino, Lo Spagna and other painters, but was stripped of them during the 19th century requisition of church property. However, it has kept some 17th century frescoes and several altarpieces from the following centuries. On the right hand wall is the splendid triptych depicting the passing away of St Francis. The great Perugian master Gerardo Dottori painted it in 1923 and donated it to the brethren of the convent in 1971.

Next to the church is the 15th century “San Bernardino” cloister. Guided by a Friar, one can visit, on the upper floor, the ancient convent. In its narrow corridor are the poor and bare cells once lived in by friars.
Passing through the cloisters, one comes to the Oratory of Blessed Giles, built on the old hermitage where the saint lived for over thirty years and where he died on the 23rd of April 1262. On the wall, in an ancient painting of the Crucifixion, there is a picture of Giles, gaunt and penitent, his eyes blazing.