The original structure of the church, dating back to at least the 9th century, it consisted of a small, almost square room corresponding to the central bay, it featured an attached square-shaped sanctuary and a partially underground crypt, which was built as structural support for the upper church that extended out over the rocks emerging along the hillside slope. Later, probably during the course of the 12th century, when a Rectory was established alongside the church and the territorial importance of the building was thus extended, massive structural changes became necessary: at first, the church was expanded by adding the entrance bay, which extended the floor plan westward and doubled the capacity of the building itself ; later a large frescoed dome is inserted into the bay that formed the original church, under which a baptismal font is placed.
This last modification makes San Salvatore a unique example throughout the national territory. In the Middle Ages, only the most imposing churches serving as the head of parishes had the authority to administer the sacrament of baptism for this purpose, a separate octagonal building was indeed built next to the church. The parish to which the Barzanò territory refers is Missaglia, which already had its own baptistery for the use of all the villages in the parish. However, perhaps due to the presence of the Rectory and certainly by episcopal permission, the small church of Barzanò also obtained the authority and privilege to administer the sacrament. This unusual grant for a small rural church is well described by the architecture, through the addition of a monumental dome with the purpose of create a spatial, visual, and symbolic focal point suitable for hosting the baptismal rite. The baptismal font of San Salvatore is composed of eight slabs of red Verona marble, set on an octagonal granite base. This base still bears the imprints of columns, now disappeared, that used to support a crown or canopy.
The baptismal font is not the only exceptional feature; it is indeed rare to find a crypt in a church of this size elsewhere in Italy. Built along the slope of the hill, the crypt has an irregular shape and is divided into two areas by an elliptical central pillar. The first area, where the two access staircases are located, serves as an antechamber and a place of welcoming the pilgrims who came here to pay their respects to the relics. These were kept in the second room, set up with two altars, of which only the one dedicated to the Virgin Mary survives. The other altar was indeed destroyed to create an opening for access to a new room added to the east, as desired by Carlo Borromeo, with the purpose of serving as a sacristy. The altar wall that still exists was entirely covered by the 13th-century fresco of the Annunciation, of which only the figure of the Virgin survives today.