The first documents about the church of St. Peter are dating back to the last years of the 10th century; however it is given that the actual aspect is the results of a large restructuring work realized around 1255 after Christ.

In fact, in some communal codes is evocated the fact that it was Innocent IV in 1254 after Christ who celebrated the consecration of the church in the same occasion when were consecrated the cathedral of San Rufino and the basilica of San Francesco. The church shows the typical map of the roman-Umbrian edifice of the 13th century, with the characteristic signs of the Benedictine order, even more obvious if one thinks about the tympanum that was originally placed on the top of the façade and that was demolished after an earthquake during the 19th century. Even it may seem irrelevant, we have to underline how the belonging to the Benedictine order is for this edifice the sign of major identity in the panorama of the other places of cult of Assisi; in fact, after an decree of the 13th century, any religious order that was not Franciscan was not allowed any more to build in the city. The rectangular façade, realized in the characteristic pink rock of the Subasio Mount, is divided horizontally by a cornice work and vertically by pilaster strips, in such a way to separate the superior areas and the three inferior ones respectively occupied by rosettes and entrance doors.
The austere internal part, in rock, is divided in three bays with a presbytery slightly elevated and a crypt; from the three apses that were originally the superior part of the church, only two are still accessible. The cupola, which during a certain period was also decorated with enamels in terracotta, has a form due to a structure, nowadays visible, made of a series of concentric stairs.