Located in an isolated position (6 km from Assisi) in the woods of Mount Subasio it was documented for the first time in 1051 along with the abbey of Farfa in Sabina; within this period must the construction of the building must have already been completed , since the architectural lines date back to the first half of the eleventh century.

San Benedetto al Subasio knew a certain splendor between the XII and XIII century when its abbots controlled more than thirty churches and chapels in the Spoleto Valley between Assisi and Foligno. In the fourteenth century, it began an unstoppable decline that led the monks to leave the abbey. The Romanesque church has perimeter walls and a presbytery with a beautiful crypt as an oratory. In archaeological excavations carried out in 1945 a second crypt supported by three columns has been brought to light, which has been indicated as the oldest part of the monastery, dating back from the X century.

The first information about the church dedicated to St. Peter date back to the second half of the tenth century. It is considered that the current building is the result of a radical restructuring, which took place around the middle of the thirteenth century. It is documented that the church was consecrated by Pope Innocent IV in 1254, together with the Cathedral of San Rufino and the great Basilica of St Francis.

The church has a Romanesque-Umbrian building plan of the thirteenth century, with the typical signs of the Benedictine order. Belonging to the order of St. Benedict gives the building an important distinguishing mark: in fact, an edict of the thirteenth century stated that in Assisi places of worship could only be built by the Franciscans.