The interior is divided into three naves. These are covered with vaults on both sides and in the center, the nave is covered with a barrel vault with lunettes. Besides the delicate decorations in light stucco on a blue background we can also see three frescoes: "The catechumens baptized"; "The glory of Saints Alfio, Filadelfo and Cirino"; "St. Andrew consacrating the bishop Neofito". Natural light filtering through the windows illuminates the three aisles.
The three windows on the facade of the building, have stained glass representations depicting St. Peter and St. Andrew with Saint Alfio in the center.
The main nave is separated from the others by arches, six on one side and six on the other. The 12 arches symbolize the 12 apostles.
The nave ends with the main altar in a big apse. By intersectioning the transept it draws the Cross of Christ.
At the intersection point the dome rises, resting on spherical plumes where the four evangelists are represented.
As in many Baroque churches, the interior ideally extends outwards, becoming almost part of the urban space, almost forcing passers-by to have a look at the square and drawing the eye towards the most important point of the church, the tabernacle.