The construction of the cloister and convent buildings on the right side of the church also dates back to those centuries. In 1958, a particularly invasive restoration brought the interior back to its original Romanesque appearance, although the interesting 18th-century decoration was lost.

The church has three very narrow and high naves, divided by two rows of circular pillars in the Lombard tradition; absent the transept, the nave ends in a triconca apse. The presbytery is strongly raised with an access staircase restored during the 20th century restoration.

The nave is covered with a lowered barrel vault, while the side aisles are cross-vaulted. A triumphal arch dividing the space of the nave from that of the presbytery is pierced by a mullioned window in the centre. The three apses, externally, present a particular decoration that divides them with thin pilasters resting on a high base and culminating in hanging arches.

A jewel of Romanesque architecture in Umbria, the crypt "ad oratorium", is divided into three apsidal naves covered with cross vaults, the central one of which is in turn tripartite with six columns of various types with re-used Roman capitals, with curious depictions of animals and plant motifs.

Behind the altar is the sarcophagus of Saint Felix the Martyr, resting on small columns that hold it suspended from the ground. The information we have about the saint is still uncertain. We know that he was bishop of Vicus ad Martis between the end of the 3rd and the beginning of the 4th century AD. but there are different versions of his martyrdom, which took place at the hands of the prefect Tarquinius presumably between 304 and 306 AD. It is said that, by divine intervention, he struggled to die despite the terrible tortures to which he was subjected: immersed in a pot of boiling pitch, placed on hot coals like St Laurence, finally beheaded.

Today, the ancient practice of invoking healing by crawling on the ground under the body of the thaumaturge saint is still in use among the faithful.

The rectangular-plan cloister has a portico supported by solid square brick pillars; above each pillar are frescoes of busts of saints and blesseds, while the frescoes on the walls depict stories from the life of Saint Felix. In the centre of the cloister is a cistern for collecting rainwater. Since 1815, the Abbey of San Felice has been the seat of the Congregation of the Precious Blood, founded by Saint Joseph del Bufalo.